Direct Cleavage Research Articles

Osteopontin as a novel substrate for the proprotein convertase 5/6 (PCSK5) in bone

Seven proprotein convertases cleave the basic amino acid consensus sequence K/R-Xn-K/R↓ (where n=0, 2, 4 or 6 variable amino acids) to activate precursor proteins. Despite similarities in substrate specificity, basic amino acid-specific proprotein convertases have a distinct tissue distribution allowing for enzymatic actions on tissue-resident substrates. Proprotein convertase 5/6 (PC5/6) has two splice variants – soluble PC5/6A and membrane-bound PC5/6B – and is expressed during mouse development in many tissues including bone and tooth, but little is known about the substrates for PC5/6 therein. Osteopontin (OPN) is an abundant bone extracellular matrix protein with roles in mineralization, cell adhesion and cell migration, and it has putative consensus sequence sites for cleavage by PC5/6, which may modify its function in bone. Since PC5/6-knockout mouse embryos show developmental abnormalities, and reduced overall mineralization, we designed this study to determine whether OPN is a substrate of PC5/6. In silico analysis of OPN protein sequences identified four potential PC5/6 consensus cleavage sites in human OPN, and three sites – including a noncanonical sequence – in mouse OPN. Ex vivo co-transfections with human OPN revealed complete OPN cleavage reducing full-length OPN (~70kDa) to an N-terminal fragment migrating at ~50kDa and two C-terminal fragments at ~18kDa and ~16kDa. Direct cleavage of OPN by PC5/6A – the predominant isoform expressed in human osteoblast cells – was confirmed by cell-free enzyme-substrate assays and by mass spectrometry. The latter was also used to investigate potential cleavage sites. Co-transfections of PC5/6 and mouse OPN showed partial cleavage of OPN into a C-terminal OPN fragment migrating at ~30kDa and an N-terminal fragment migrating at ~29kDa. Micro-computed tomography of PC5/6-knockout embryos at E18.5 confirmed a reduction in mineralized bone, and in situ hybridization performed on cryo-sections of normal mouse bone using Pcsk5 and Opn anti-sense and control-sense cRNA probes indicated the co-localization of the expression of these genes in bone cells. This mRNA expression profile was supported by semi-quantitative RT-PCR using osteoblast primary cultures, and cultured MC3T3-E1 osteoblast and MLO-Y4 osteocyte cell lines. Immunoblotting for OPN from mouse bone extracts showed altered OPN processing in PC5/6-knockout mice compared to wildtype mice. OPN fragments migrated at ~25kDa and ~16kDa in wildtype bone and were not present in PC5/6-deficient bone. In conclusion, this study demonstrates that Pcsk5 is expressed in bone-forming cells, and that OPN is a novel substrate for PC5/6. Cleavage of OPN by PC5/6 may modify the function of OPN in bone and/or modulate other enzymatic cleavages of OPN, leading to alterations in the bone phenotype.

Pronuclear pattern does not predict morphokinetics behavior in human embryos

The purpose was to investigate the correlation between pronuclei (PN) morphology and morphokinetic behaviors of derived embryos with time lapse monitoring (TLM) in assisted reproduction setting. Over time, PN morphology from PN appearance (PNA) to PN fading (PNF), PNF according to size, contact, number and position of nuclear precursor bodies (NPBs) within each PN and morphokinetics variables, including absolute time points, relative timing parameters, cleavage patterns and arrest rate, were evaluated using TLM. There were insignificant relationship between morphokinetics variables including tBP2, tPNA, tPNF, t2, t3, t4, t5, t6, t7, t8, S1, CC2, S2 and Z scoring according Z1 to Z4 (p > .05). Also, an insignificant relationship was noticed between uneven blastomeres, reverse cleavage embryos and Z scoring (p > .05). However, there were significant correlations between the rates of direct and arbitrary cleavage as well as arrested embryos and Z scores. Combined PN morphology and embryo kinetic evaluation were suggested in assisted reproduction programs.

A Theoretical Study of Chemical Reactivity of Tartrazine Through DFT Reactivity Descriptors

<p>In this work we have calculated global and local DFT reactivity descriptors for tartrazine at B3LYP/6-311++G (2d,2p) level. Global reactivity descriptors such as ionization energy, molecular hardness, electrophilicity, and total energies were calculated to evaluate the tartrazine reactivity in aqueous and gas conditions. Local reactivity was evaluated through the Fukui function. The influence of the solvent was taken into account with the PCM model. The results indicate that the solvation process modifies the reactivity descriptors values. From our results, it was found that an electrophilic attack allows a direct cleavage of the N=N bond. If a nucleophilic attack is considered as initial attack, it is necessary a second attack by free radicals or electrophiles to cleave the N=N bond. In the case of an initial attack by free radicals, tartrazine requires a subsequent nucleophilic attack to cleave the N=N bond.</p>

Prolonged seizure activity causes caspase dependent cleavage and dysfunction of G-protein activated inwardly rectifying potassium channels

Recurrent high-frequency epileptic seizures cause progressive hippocampal sclerosis, which is associated with caspase-3 activation and NMDA receptor-dependent excitotoxicity. However, the identity of caspase-3 substrates that contribute to seizure-induced hippocampal atrophy remains largely unknown. Here, we show that prolonged high-frequency epileptiform discharges in cultured hippocampal neurons leads to caspase-dependent cleavage of GIRK1 and GIRK2, the major subunits of neuronal G protein-activated inwardly rectifying potassium (GIRK) channels that mediate membrane hyperpolarization and synaptic inhibition in the brain. We have identified caspase-3 cleavage sites in GIRK1 (387ECLD390) and GIRK2 (349YEVD352). The YEVD motif is highly conserved in GIRK2-4, and located within their C-terminal binding sites for Gβγ proteins that mediate membrane-delimited GIRK activation. Indeed, the cleaved GIRK2 displays reduced binding to Gβγ and cannot coassemble with GIRK1. Loss of an ER export motif upon cleavage of GIRK2 abolishes surface and current expression of GIRK2 homotetramic channels. Lastly, kainate-induced status epilepticus causes GIRK1 and GIRK2 cleavage in the hippocampus in vivo. Our findings are the first to show direct cleavage of GIRK1 and GIRK2 subunits by caspase-3, and suggest the possible role of caspase-3 mediated down-regulation of GIRK channel function and expression in hippocampal neuronal injury during prolonged epileptic seizures.

3′ RNA ligase mediated rapid amplification of cDNA ends for validating viroid induced cleavage at the 3′ extremity of the host mRNA

5′ RNA ligase-mediated rapid amplification of cDNA ends (5′ RLM-RACE) is a widely-accepted method for the validation of direct cleavage of a target gene by a microRNA (miRNA) and viroid-derived small RNA (vd-sRNA). However, this method cannot be used if cleavage takes place in the 3′ extremity of the target RNA, as this gives insufficient sequence length to design nested PCR primers for 5′ RLM RACE. To overcome this hurdle, we have developed 3′ RNA ligase-mediated rapid amplification of cDNA ends (3′ RLM RACE). In this method, an oligonucleotide adapter having 5′ adenylated and 3′ blocked is ligated to the 3′ end of the cleaved RNA followed by PCR amplification using gene specific primers. In other words, in 3′ RLM RACE, 3′ end is mapped using 5′ fragment instead of small 3′ fragment. The method developed here was verified by examining the bioinformatics predicted and parallel analysis of RNA ends (PARE) proved cleavage sites of chloride channel protein CLC-b-like mRNA in Potato spindle tuber viroid infected tomato plants. The 3′ RLM RACE developed in this study has the potential to validate the miRNA and vd-sRNA mediated cleavage of mRNAs at its 3′ untranslated region (3′ UTR).

Controlling phenolic hydrodeoxygenation by tailoring metal–O bond strength via specific catalyst metal type and particle size selection

Experimental and theoretical studies of hydrodeoxygenation (HDO) of m-cresol show that on metals of low oxophilicity, such as Pt or Pd, the direct CO bond cleavage is not possible. Therefore, HDO requires an indirect pathway via tautomerization. In contrast, on metals of higher oxophilicity, such as Ru or Rh, the direct CO bond cleavage is possible and toluene can be directly obtained from m-cresol. These studies show that the HDO activity correlates directly with the metal oxophilicity, which in turn depends on the position of the d-band center relative to the Fermi level. This catalytic descriptor depends on (1) the type of metal and (2) the extent of coordination of the metal atoms. The present contribution investigates the effect of the second factor. It is demonstrated that a Rh/SiO2 catalyst with small particles (low-coordination sites) is more active for HDO than one with larger particles (high-coordination sites). At the same time, the low coordination site is more prone to deactivation and loss of HDO selectivity. These experimental results are combined with the density functional theory calculations, which show that the energy barrier for direct CO bond cleavage is lower on a step site than on a terrace site. At the same time, it is shown that a step site requires a higher energy barrier to remove adsorbed molecular fragments to regenerate the activity than a terrace site, which explains the faster deactivation rate observed on catalysts with small more defective metal clusters.

Deconstructing the Lectin Pathway in the Pathogenesis of Experimental Inflammatory Arthritis: Essential Role of the Lectin Ficolin B and Mannose-Binding Protein-Associated Serine Protease 2.

Complement plays an important role in the pathogenesis of rheumatoid arthritis. Although the alternative pathway (AP) is known to play a key pathogenic role in models of rheumatoid arthritis, the importance of the lectin pathway (LP) pattern recognition molecules such as ficolin (FCN) A, FCN B, and collectin (CL)-11, as well as the activating enzyme mannose-binding lectin-associated serine protease-2 (MASP-2), are less well understood. We show in this article that FCN A-/- and CL-11-/- mice are fully susceptible to collagen Ab-induced arthritis (CAIA). In contrast, FCN B-/- and MASP-2-/-/sMAp-/- mice are substantially protected, with clinical disease activity decreased significantly (p < 0.05) by 47 and 70%, respectively. Histopathology scores, C3, factor D, FCN B deposition, and infiltration of synovial macrophages and neutrophils were similarly decreased in FCN B-/- and MASP-2-/-/sMAp-/- mice. Our data support that FCN B plays an important role in the development of CAIA, likely through ligand recognition in the joint and MASP activation, and that MASP-2 also contributes to the development of CAIA, likely in a C4-independent manner. Decreased AP activity in the sera from FCN B-/- and MASP-2-/-/sMAp-/- mice with arthritis on adherent anti-collagen Abs also support the hypothesis that pathogenic Abs, as well as additional inflammation-related ligands, are recognized by the LP and operate in vivo to activate complement. Finally, we also speculate that the residual disease seen in our studies is driven by the AP and/or the C2/C4 bypass pathway via the direct cleavage of C3 through an LP-dependent mechanism.

Catalytic Nitrogen Fixation via Direct Cleavage of Nitrogen–Nitrogen Triple Bond of Molecular Dinitrogen under Ambient Reaction Conditions

Abstract We have now found that molybdenum–iodide complexes bearing a PNP-pincer ligand have a higher catalytic activity than the so far reported molybdenum–dinitrogen complexes for ammonia formation from nitrogen gas under ambient reaction conditions, up to 830 equiv being produced based on a dinitrogen-bridged dimolybdenum complex (415 equiv of ammonia based on the molybdenum atom). This remarkable catalytic activity is induced by a novel reaction pathway, where the generation of a dinitrogen-bridged dimolybdenum–iodide complex is a key point to promote direct cleavage of the nitrogen–nitrogen triple bond of the bridging dinitrogen ligand in the Mo–N≡N–Mo core.

Abstract 4597: A novel immuno-oncology approach: targeting cell-surface mesothelin with a fusion construct containing human granzyme B

Abstract Immunological approaches to target tumors have gained considerable traction recently because of excellent clinical results. In addition, targeted treatment with antibody-drug conjugates (ADCs) can also be effective in achieving regression of solid tumors. The challenge for ADCs continues to be efficacy, stability of the construct and development of resistance. We have developed a unique fusion protein composed of 1) a novel human single-domain antibody (SD1) that uniquely targets Region III of the mesothelin glycoprotein and 2) an engineered version of the human serine protease Granzyme B (GrB). Mesothelin is highly expressed in aggressive cancers such as malignant mesothelioma, pancreatic and ovarian cancers, and NSCLC. Granzyme B generates an intense, irreversible pro-apoptotic effect through direct cleavage of caspases, release of cytochrome C from mitochrondria, and cleavage of nuclear matrix. Previous ADCs targeting mesothelin have faced the drawbacks of toxic payloads, formation of neutralizing antibodies, and competition with the serum protein MUC16/CA125. SD1-GrB represents a new class of completely human immunotoxins containing a payload with a unique mechanism of action. Additionally, because of its unique binding properties, SD1 does not compete with circulating CA125 and is not subject to cleavage. The SD1-GrB construct was designed as a homodimer (~200kDa) containing an IgG Fc domain and was expressed using transient-transfection of HEK293E cells. The soluble SD1-GrB was isolated from conditioned media and purified to homogeneity as assessed by SDS-PAGE and Western. Enzymatic activity of the GrB component was assessed by IEPD and found to be similar to authentic, native GrB. Binding to mesothelin was confirmed by surface plasmon resonance. Additionally, binding to the human lung adenocarcinoma cell lines H460 and HCC1703 was demonstrated by ELISA. Initial cytotoxicity (IC50) of SD1-GrB against H460 and HCC1703 was in the 30 nM range. Assessment against a larger panel of cell lines is ongoing followed by in vivo efficacy in a human tumor xenograft model. Our preliminary evaluation of SD1-GrB ADC suggests this construct has a unique mechanism of action and is highly cytotoxic against target cells. This molecule appears to be an excellent candidate for further pre-clinical development as a therapeutic agent. Research conducted, in part, by the Clayton Foundation for Research. Citation Format: Lawrence H. Cheung, Rasheed Tijani, Nasir Khan, Claire Thuning-Roberson, Michael G. Rosenblum. A novel immuno-oncology approach: targeting cell-surface mesothelin with a fusion construct containing human granzyme B [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4597. doi:10.1158/1538-7445.AM2017-4597

Prospective study of automated versus manual annotation of early time-lapse markers in the human preimplantation embryo.

How does automated time-lapse annotation (Eeva™) compare to manual annotation of the same video images performed by embryologists certified in measuring durations of the 2-cell (P2; time to the 3-cell minus time to the 2-cell, or t3-t2) and 3-cell (P3; time to 4-cell minus time to the 3-cell, or t4-t3) stages? Manual annotation was superior to the automated annotation provided by Eeva™ version 2.2, because manual annotation assigned a rating to a higher proportion of embryos and yielded a greater sensitivity for blastocyst prediction than automated annotation. While use of the Eeva™ test has been shown to improve an embryologist's ability to predict blastocyst formation compared to Day 3 morphology alone, the accuracy of the automated image analysis employed by the Eeva™ system has never been compared to manual annotation of the same time-lapse markers by a trained embryologist. We conducted a prospective cohort study of embryos (n = 1477) cultured in the Eeva™ system (n = 8 microscopes) at our institution from August 2014 to February 2016. Embryos were assigned a blastocyst prediction rating of High (H), Medium (M), Low (L), or Not Rated (NR) by Eeva™ version 2.2 according to P2 and P3. An embryologist from a team of 10, then manually annotated each embryo and if the automated and manual ratings differed, a second embryologist independently annotated the embryo. If both embryologists disagreed with the automated Eeva™ rating, then the rating was classified as discordant. If the second embryologist agreed with the automated Eeva™ score, the rating was not considered discordant. Spearman's correlation (ρ), weighted kappa statistics and the intra-class correlation (ICC) coefficients with 95% confidence intervals (CI) between Eeva™ and manual annotation were calculated, as were the proportions of discordant embryos, and the sensitivity, specificity, positive predictive value (PPV) and NPV of each method for blastocyst prediction. The distribution of H, M and L ratings differed by annotation method (P < 0.0001). The correlation between Eeva™ and manual annotation was higher for P2 (ρ = 0.75; ICC = 0.82; 95% CI 0.82-0.83) than for P3 (ρ = 0.39; ICC = 0.20; 95% CI 0.16-0.26). Eeva™ was more likely than an embryologist to rate an embryo as NR (11.1% vs. 3.0%, P < 0.0001). Discordance occurred in 30.0% (443/1477) of all embryos and was not associated with factors such as Day 3 cell number, fragmentation, symmetry or presence of abnormal cleavage. Rather, discordance was associated with direct cleavage (P2 ≤ 5 h) and short P3 (≤0.25 h), and also factors intrinsic to the Eeva™ system, such as the automated rating (proportion of discordant embryos by rating: H: 9.3%; M: 18.1%; L: 41.3%; NR: 31.4%; P < 0.0001), microwell location (peripheral: 31.2%; central: 23.8%; P = 0.02) and Eeva™ microscope (n = 8; range 22.9-42.6%; P < 0.0001). Manual annotation upgraded 82.6% of all discordant embryos from a lower to a higher rating, and improved the sensitivity for predicting blastocyst formation. One team of embryologists performed the manual annotations; however, the study staff was trained and certified by the company sponsor. Only two time-lapse markers were evaluated, so the results are not generalizable to other parameters; likewise, the results are not generalizable to future versions of Eeva™ or other automated image analysis systems. Based on the proportion of discordance and the improved performance of manual annotation, clinics using the Eeva™ system should consider manual annotation of P2 and P3 to confirm the automated ratings generated by Eeva™. These data were acquired in a study funded by Progyny, Inc. There are no competing interests. N/A.

Elucidation of reaction mechanism for m-cresol hydrodeoxygenation over Fe based catalysts: A kinetic study

Fe based catalysts are promising for hydrodeoxygenation (HDO) of lignin derived phenolics due to their high selectivity for aromatics. In this work, the reaction mechanism of m-cresol HDO on Fe catalysts and the kinetic consequence with Pd addition were elucidated by examining the effect of H2, H2O and m-cresol pressures on toluene formation rate on Fe and PdFe catalysts. A direct CO bond cleavage mechanism is proposed for HDO catalysis on both Fe and PdFe catalysts, while Pd provides a facilitated reaction pathway at the PdFe interface and therefore promotes the catalysis on Fe without changing the high selectivity towards aromatics.

Expression dynamics of Glycine max (L.) Merrill microRNAs (miRNAs) and their targets during Mungbean yellow mosaic India virus (MYMIV) infection

MicroRNAs (miRNAs) are class of small non coding RNAs (sncRNAs) that modulate gene regulatory mechanisms including conferring antiviral resistance in plants. Expressional changes of selected conserved miRNAs and putatively antiviral miRNAs were analyzed in two soybean genotypes (JS335 and UPSM534) with contrasting disease reaction trait against Mungbean yellow mosaic India virus (MYMIV) family Geminiviridae. Expression profiling of conserved miRNAs and corresponding target mRNAs in both the soybean genotypes suggests the role of Argonaute homeostasis in virus resistance along with the gene regulatory changes in hormonal signaling pathways. Putative antiviral miRNAs displayed upregulation upon MYMIV infection in both the soybean genotypes. Further, experimental evidence prove that soybean derived miRNA potentially target and direct cleavage of MYMIV mRNA encoding movement protein (BC1). Thus, this work provides molecular insights regarding changes in expression of miRNAs during MYMIV infection and improves deeper understanding of role of soybean miRNAs in MYMIV resistance. To the best of our knowledge this is the first report of soybean derived miRNAs exhibiting potential antiviral resistance during begomovirus infection.

Controlling the anaphylatoxin C5a in diseases requires a specifically targeted inhibition

The terminal complement split product C5a has been described as an important mediator in inflammatory diseases. C5a is generated upon cleavage of C5 and earlier research suggests that, besides the known C5 convertases formed upon activation of the complement pathways, various enzymes could activate C5 directly. We demonstrate that eculizumab effectively blocks C5 activation when mediated by C5-convertase formation, but fails to block C5a generation resulting from direct enzymatic cleavage by trypsin and thrombin. C5a generated by these enzymes is shown to be fully biologically functional and can be blocked by IFX-1, a specific monoclonal anti-human C5a antibody. We further report clinical cases of atypical hemolytic uremic syndrome (aHUS) and C3 Glomerulonephritis (C3GN) patients under treatment with eculizumab presenting substantially elevated C5a levels. Thus, blocking the C5 convertase mediated activation of C5 may not be efficient to control C5a-mediated effects in human disease and that a targeted approach is warranted.

Transgenic Clustered Regularly Interspaced Short Palindromic Repeat/Cas9-Mediated Viral Gene Targeting for Antiviral Therapy of Bombyx mori Nucleopolyhedrovirus.

ABSTRACTWe developed a novel antiviral strategy by combining transposon-based transgenesis and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system for the direct cleavage of Bombyx mori nucleopolyhedrovirus (BmNPV) genome DNA to promote virus clearance in silkworms. We demonstrate that transgenic silkworms constitutively expressing Cas9 and guide RNAs targeting the BmNPV immediate early-1 (ie-1) and me53 genes effectively induce target-specific cleavage and subsequent mutagenesis, especially large (∼7-kbp) segment deletions in BmNPV genomes, and thus exhibit robust suppression of BmNPV proliferation. Transgenic animals exhibited higher and inheritable resistance to BmNPV infection than wild-type animals. Our approach will not only contribute to modern sericulture but also shed light on future antiviral therapy.IMPORTANCE Pathogen genome targeting has shown its potential in antiviral research. However, transgenic CRISPR/Cas9 system-mediated viral genome targeting has not been reported as an antiviral strategy in a natural animal host of a virus. Our data provide an effective approach against BmNPV infection in a real-world biological system and demonstrate the potential of transgenic CRISPR/Cas9 systems in antiviral research in other species.

MCPIP1, alias Regnase-1 binds and cleaves mRNA of C/EBPβ.

CCAAT/enhancer-binding protein beta (C/EBPβ) is a transcription factor controlling a broad range of genes essential for homeostasis, including genes related to immune functions, inflammation, metabolism and growth. Monocyte chemoattractant protein-1-induced protein 1 (MCPIP1) also called as Regnase-1 is an RNase and has been shown to decrease the stability of short-lived transcripts coding for inflammation-related proteins, including IL-1β, IL-6, IL-2, IL-8, IL-12b, IER-3, c-Rel. We found previously that the half-life of the C/EBPβ transcript is regulated by MCPIP. To understand the mechanism driving down-regulation of C/EBPβ by MCPIP1, we applied an in vitro cleavage assay, followed by a luciferase-reporter assay and RNA immunoprecipitation (RIP). We demonstrated that MCPIP1 recognizes regions of the 3’UTR of C/EBPβ mRNA and promotes its decay by introducing direct endonucleolytic cleavage.

Preliminary investigation of the prevalence and implantation potential of abnormal embryonic phenotypes assessed using time-lapse imaging

This retrospective, single site observational study aimed to delineate five abnormal embryonic developmental phenotypes, assessing their prevalence, development potential and suitability for inclusion in embryo selection models for IVF. In total, 15,819 embryos from 4559 treatment cycles cultured in EmbryoScope® incubators between January 2014 and January 2016 were included. Time-lapse images were assessed retrospectively for five abnormal embryo phenotypes: direct cleavage, reverse cleavage, absent cleavage, chaotic cleavage and cell lysis. The prevalence of each abnormal phenotype was assessed. Final embryo disposition, embryo quality and implantation rate were determined and compared with a control embryo cohort. The collective prevalence for the five abnormal phenotypes was 11.4%; chaotic cleavage and direct cleavage together constituted 9.7%. Implantation rates were 17.4%, 0%, 25%, 2.1% and 0% for direct, reverse, absent, chaotic cleavage and cell lysis, respectively. The overall implantation rate for all abnormal embryos with known implantation status was significantly lower compared with the control population (6.9% versus 38.7%, P < 0.0001). The proportion of good quality embryos in each category of abnormal cleavage remained below 25%. Embryos exhibiting an abnormal phenotype may have reduced developmental capability, manifested in both embryo quality and implantation potential, when compared with embryos of normal phenotype.

TRNA-derived small RNAs target transposable element transcripts.

tRNA-derived RNA fragments (tRFs) are 18–26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are processed by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA. We utilized the fact that many plant small RNAs direct cleavage of their target transcripts to demonstrate that the tRF–AGO1 complex acts to specifically target and cleave endogenous transposable element (TE) mRNAs produced from transcriptionally active TEs. The data presented here demonstrate that tRFs are bona-fide regulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.

Mechanistic analysis of the role of metal oxophilicity in the hydrodeoxygenation of anisole

A combined experimental and theoretical comparative study of the hydrodeoxygenation (HDO) of anisole was conducted over Pt, Ru, and Fe metals. In the experimental part, an inert silica support was used to directly compare the catalytic activity and selectivity of the three metals at 375°C under H2 flow at atmospheric pressure. In parallel, for density functional theory (DFT) calculations the close-packed Pt(111), Ru(0001), and Fe(110) surfaces were employed to compare the possible mechanisms on these metals. It was observed that over Pt/SiO2 and Ru/SiO2 catalysts, both phenol and benzene were the major products in a phenol/benzene ratio that decreased with the level of conversion. By contrast, over the Fe/SiO2 catalyst, no phenol formation was detected, even at low conversions. The DFT results show that over all the three metal surfaces the dehydrogenation at the CH3 side group occurs before the CO bond breaking. This removal of H atoms from the CH3 group facilitates the activation of the aliphatic CalkylO bond. Therefore, it can be concluded that a common intermediate for the three metals is a surface phenoxy and the significant differences between the three metals are related to the reactivity of this surface phenoxy. That is, over Pt(111) and Ru(0001) the phenoxy intermediate is hydrogenated to phenol, which in turn, can undergo further HDO to form benzene. This result is in agreement with the experiments over Pt/SiO2 and Ru/SiO2 catalysts. Over these catalysts, both phenol and benzene are major products, with the selectivity to benzene increasing with conversion at the expense of phenol. In contrast, over the Fe(110) surface, the strong metal oxophilicity makes the direct cleavage of the CO bond in the surface phenoxy easier than hydrogenation to phenol. Thus, it is predicted that phenol is not formed over iron, but only benzene should be observed as HDO product at all conversion levels, which is also in agreement with the experimental observations.

Theoretical Study on Reaction Pathways Leading to CO and CO2 in the Pyrolysis of Resorcinol.

Possible pathways for the pyrolysis of resorcinol with the formation of CO and CO2 as final products were proposed and evaluated using ab initio calculations. Our experimental study revealed that large quantities of CO2 are generated in the pyrolysis of 1,3-dihydroxybenzene (resorcinol), while the pyrolysis of the dihydroxybenzene isomers 1,2-dihydroxybenzene (catechol) and 1,4-dihydroxybenzene (hydroquinone) produces little CO2. The fate of oxygen atoms in catechol and hydroquinone was essentially the formation of CO. In the proposed pathways, the triplet ground state m-benzoquinone was generated initially from simultaneous cleavage of the two O-H bonds in resorcinol. Subsequently, the direct cleavage of a C-C bond of the m-benzoquinone diradical yields 2-oxidanylcyclopenta-2,4-dien-1-yl-methanone, which can be converted via two channels: release of CO from the aldehyde radical group and combination of the ketone radical and carbon atom in the aldehyde radical group to form the 6-oxabicyclo[3.2.0]hepta-2,4-dien-7-one, resulting in the release of CO2. Potential energy surfaces along the proposed reaction pathways were calculated employing the CBS-QB3 method, and the rate constants at the high-pressure limit were also evaluated based on transition-state theory to assess the feasibility of the proposed reaction pathways.

Evaluation of human embryo development in in vitro fertilization- and intracytoplasmic sperm injection-fertilized oocytes: A time-lapse study.

ObjectiveWe investigated whether the insemination method (in vitro fertilization [IVF] or intracytoplasmic sperm injection [ICSI]) affected morphokinetic events and abnormal cleavage events in embryonic development.MethodsA total of 1,830 normal fertilized embryos were obtained from 272 IVF and ICSI cycles that underwent ovum retrieval culture using a time-lapse system (Embryoscope) from June 2013 to March 2015. All embryos were investigated by a detailed time-lapse analysis that measured the developmental events in the hours after IVF or ICSI insemination.ResultsNo significant differences were observed between the two groups regarding clinical outcomes (p>0.05). ICSI-derived embryos showed significantly faster morphokinetics than those derived from conventional IVF, from the time to pronuclear fading to the time to 6 cells (p<0.05). However, no significant differences were found from the time to 7 cells to the time to expanded blastocyst (p>0.05). There were no differences in abnormal cleavage events between the two groups (p>0.05); they showed the same rates of direct cleavage from 1 to 3 cells, 2 multinucleated cells, 2 uneven cells, and reverse cleavage.ConclusionThe morphokinetics of embryo development was found to vary between IVF- and ICSI-fertilized oocytes, at least until the 6-cell stage. However, these differences did not affect the clinical outcomes of the embryo. Additionally, no significant differences in abnormal cleavage events were found according to the fertilization method.