bluuebunny/crossref_metadata_2025_split huggingface dataset:
A scalable and operationally simple radical trifluoromethylation
Authors: Beatty Joel W. , Douglas James J. , Cole Kevin P. , Stephenson Corey R. J. 
Published: August 2015

AbstractThe large number of reagents that have been developed for the synthesis of trifluoromethylated compounds is a testament to the importance of the CF3 group as well as the associated synthetic challenge. Current state-of-the-art reagents for appending the CF3 functionality directly are highly effective; however, their use on preparative scale has minimal precedent because they require multistep synthesis for their preparation, and/or are prohibitively expensive for large-scale application. For a scalable trifluoromethylation methodology, trifluoroacetic acid and its anhydride represent an attractive solution in terms of cost and availability; however, because of the exceedingly high oxidation potential of trifluoroacetate, previous endeavours to use this material as a CF3 source have required the use of highly forcing conditions. Here we report a strategy for the use of trifluoroacetic anhydride for a scalable and operationally simple trifluoromethylation reaction using pyridine N-oxide and photoredox catalysis to affect a facile decarboxylation to the CF3 radical.
DNA/RNA heteroduplex oligonucleotide for highly efficient gene silencing
Authors: Nishina Kazutaka , Piao Wenying , Yoshida-Tanaka Kie , Sujino Yumiko , Nishina Tomoko , Yamamoto Tsuyoshi , Nitta Keiko , Yoshioka Kotaro , Kuwahara Hiroya , Yasuhara Hidenori , Baba Takeshi , Ono Fumiko , Miyata Kanjiro , Miyake Koichi , Seth Punit P. , Low Audrey , Yoshida Masayuki , Bennett C. Frank , Kataoka Kazunori , Mizusawa Hidehiro , Obika Satoshi , Yokota Takanori 
Published: August 2015

AbstractAntisense oligonucleotides (ASOs) are recognized therapeutic agents for the modulation of specific genes at the post-transcriptional level. Similar to any medical drugs, there are opportunities to improve their efficacy and safety. Here we develop a short DNA/RNA heteroduplex oligonucleotide (HDO) with a structure different from double-stranded RNA used for short interfering RNA and single-stranded DNA used for ASO. A DNA/locked nucleotide acid gapmer duplex with an α-tocopherol-conjugated complementary RNA (Toc-HDO) is significantly more potent at reducing the expression of the targeted mRNA in liver compared with the parent single-stranded gapmer ASO. Toc-HDO also improves the phenotype in disease models more effectively. In addition, the high potency of Toc-HDO results in a reduction of liver dysfunction observed in the parent ASO at a similar silencing effect. HDO technology offers a novel concept of therapeutic oligonucleotides, and the development of this molecular design opens a new therapeutic field.
SPINK1 promotes colorectal cancer progression by downregulating Metallothioneins expression
Authors: Tiwari R , Pandey S K , Goel S , Bhatia V , Shukla S , Jing X , Dhanasekaran S M , Ateeq B 
Published: August 2015

AbstractColorectal cancer (CRC) is the third most common cancer in the world, and second leading cause of cancer deaths in the US. Although, anti-EGFR therapy is commonly prescribed for CRC, patients harboring mutations in KRAS or BRAF show poor treatment response, indicating an ardent demand for new therapeutic targets discovery. SPINK1 (serine peptidase inhibitor, Kazal type 1) overexpression has been identified in many cancers including the colon, lung, breast and prostate. Our study demonstrates the functional significance of SPINK1 in CRC progression and metastases. Stable knockdown of SPINK1 significantly decreases cell proliferation, invasion and soft agar colony formation in the colon adenocarcinoma WiDr cells. Conversely, an increase in these oncogenic phenotypes was observed on stimulation with SPINK1-enriched conditioned media (CM) in multiple benign models such as murine colonic epithelial cell lines, MSIE and YAMC (SPINK3-negative). Mechanistically, SPINK1 promotes tumorigenic phenotype by activating phosphatidylinositol 3-kinase (PI3K/AKT) and mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) signaling pathways, and the SPINK1-positive WiDr cells are sensitive to AKT and MEK inhibitors. Importantly, SPINK1 silencing mediated upregulation of various Metallothionein isoforms, considered as tumor suppressors in CRC, confer sensitivity to doxorubicin, which strengthens the rationale for using the combinatorial treatment approach for the SPINK1-positive CRC patients. Furthermore, in vivo studies using chicken chorioallantoic membrane assay, murine xenograft studies and metastasis models further suggest a pivotal role of SPINK1 in CRC progression and metastasis. Taken together, our study demonstrates an important role for the overexpressed SPINK1 in CRC disease progression, a phenomenon that needs careful evaluation towards effective therapeutic target development.
Surface Plasmon Resonance Biosensor Based on Smart Phone Platforms
Authors: Liu Yun , Liu Qiang , Chen Shimeng , Cheng Fang , Wang Hanqi , Peng Wei 
Published: August 2015

AbstractWe demonstrate a fiber optic surface plasmon resonance (SPR) biosensor based on smart phone platforms. The light-weight optical components and sensing element are connected by optical fibers on a phone case. This SPR adaptor can be conveniently installed or removed from smart phones. The measurement, control and reference channels are illuminated by the light entering the lead-in fibers from the phone’s LED flash, while the light from the end faces of the lead-out fibers is detected by the phone’s camera. The SPR-sensing element is fabricated by a light-guiding silica capillary that is stripped off its cladding and coated with 50-nm gold film. Utilizing a smart application to extract the light intensity information from the camera images, the light intensities of each channel are recorded every 0.5 s with refractive index (RI) changes. The performance of the smart phone-based SPR platform for accurate and repeatable measurements was evaluated by detecting different concentrations of antibody binding to a functionalized sensing element and the experiment results were validated through contrast experiments with a commercial SPR instrument. This cost-effective and portable SPR biosensor based on smart phones has many applications, such as medicine, health and environmental monitoring.
Unity and diversity in the human adenoviruses: exploiting alternative entry pathways for gene therapy
Authors: Hall Kathryn , Blair Zajdel Maria E. , Blair G. Eric 
Published: August 2015

Human Ads (adenoviruses) have been extensively utilized for the development of vectors for gene transfer, as they infect many cell types and do not integrate their genome into host-cell chromosomes. In addition, they have been widely studied as cytolytic viruses, termed oncolytic adenoviruses in cancer therapy. Ads are non-enveloped viruses with a linear double-stranded DNA genome of 30–38 kb which encodes 30–40 genes. At least 52 human Ad serotypes have been identified and classified into seven species, A–G. The Ad capsid has icosahedral symmetry and is composed of 252 capsomers, of which 240 are located on the facets of the capsid and consist of a trimeric hexon protein and the remaining 12 capsomers, the pentons, are at the vertices and comprise the penton base and projecting fibre protein. The entry of Ads into human cells is a two-step process. In the first step, the fibre protein mediates a primary interaction with the cell, effectively tethering the virus particle to the cell surface via a cellular attachment protein. The penton base then interacts with cell-surface integrins, leading to virus internalization. This interaction of the fibre protein with a number of cell-surface molecules appears to be important in determining the tropism of adenoviruses. Ads from all species, except species B and certain serotypes of species D, utilize CAR (coxsackie and adenovirus receptor) as their primary cellular-attachment protein, whereas most species B Ads use CD46, a complement regulatory protein. Such species-specific differences, as well as adaptations or modifications of Ads required for applications in gene therapy, form the major focus of the present review.
Conformational state of a 25-mer peptide from the cyclophilin-binding loop of the HIV type 1 capsid protein
Authors: REIMER Ulf , DREWELLO Mario , JAKOB Mario , FISCHER Gunter , SCHUTKOWSKI Mike 
Published: August 2015

Recently a 25-residue part of Gag polyprotein from HIV type 1 (HIV-1) was reported to bind to the cytosolic 18 kDa cyclophilin (Cyp18) with an IC50 value of 180 μM. This peptide corresponds to the Cyp18-binding domain of HIV-1 Gag. A replacement of Gly with Ala in the cyclophilin-binding loop of HIV-1 Gag polyprotein results in the prevention of the packaging of Cyp18 into virions. We found only two conformers of this peptide among 16 possible expected conformers, owing to cis/trans isomerization of four peptidyl-prolyl bonds. Although this finding implicates the existence of a stabilizing structure, we were not able to detect secondary structure formation by 1H-NMR and CD spectroscopy. We characterized the peptide as a substrate for Cyp18 by two-dimensional exchange 1H-NMR spectroscopy. Surprisingly, we found similar binding characteristics for a peptide corresponding to 25-mer peptide containing the above-mentioned Gly to Ala substitution.
‘GPEET’ procyclin is the major surface protein of procyclic culture forms of Trypanosoma brucei brucei strain 427
Authors: BÜTIKOFER Peter , RUEPP Stefan , BOSCHUNG Monika , RODITI Isabel 
Published: August 2015

The surface of Trypanosoma brucei brucei insect forms is covered by an invariant protein coat consisting of procyclins. There are six or seven procyclin genes that encode unusual proteins with extensive tandem repeat units of glutamic acid (E) and proline (P) (referred to as EP repeats), and two genes that encode proteins with internal pentapeptide (GPEET) repeats. Although the EP forms of procyclins have been isolated and characterized by several laboratories, evidence for GPEET procyclin has largely been confined to the expression of its mRNA. To characterize GPEET procyclin further, we isolated the protein from T. b. brucei strain 427. We found that label from [3H]myristic acid and [3H]ethanolamine was incorporated into GPEET procyclin and we demonstrated the protein's covalent modification with a glycosylphosphatidylinositol anchor. The major form of GPEET procyclin showed an apparent molecular mass of 22–32 kDa, was susceptible to proteolytic treatment and was found to be phosphorylated. Surprisingly, our results show that GPEET procyclin represents the major form of procyclin in T. b. brucei 427 culture forms and that the ratio of EP to GPEET procyclin can vary considerably between different cell lines.
Novel activity of endothelin-converting enzyme: hydrolysis of bradykinin
Authors: HOANG Mien V. , TURNER Anthony J. 
Published: August 2015

Endothelin-converting enzyme (ECE) is the key enzyme in the production of the potent vasoconstrictor endothelin from its inactive precursor big endothelin. To date, no other physiological peptide substrate has been identified for ECE. Here, by using Chinese hamster ovary (CHO) cells transfected with rat ECE-1 cDNA, we have established that ECE can hydrolyse the vasodilator bradykinin. The hydrolysis of bradykinin by ECE is exclusively at the Pro7–Phe8 bond, producing bradykinin-(1–7) and bradykinin-(8–9). Hydrolysis is completely inhibited by 100 μM phosphoramidon and 200 μM EDTA, but only slightly by the specific neprilysin inhibitor thiorphan (100 μM). The ability of ECE to act as a peptidyl dipeptidase rather than an endopeptidase in hydrolysing bradykinin suggests a much broader specificity for the enzyme than previously recognized, which may lead to the design of new and specific inhibitors of ECE and to the identification of other potential physiological substrates.
Δ-1-Piperideine-6-carboxylate dehydrogenase, a new enzyme that forms α-aminoadipate in Streptomyces clavuligerus and other cephamycin C-producing actinomycetes
Authors: de la FUENTE Juan L. , RUMBERO Angel , MARTÍN Juan F. , LIRAS Paloma 
Published: August 2015

Δ-1-Piperideine-6-carboxylate (P6C) dehydrogenase activity, which catalyses the conversion of P6C into α-aminoadipic acid, has been studied in the cephamycin C producer Streptomyces clavuligerus by both spectrophotometric and radiometric assays. The enzyme has been purified 124-fold to electrophoretic homogeneity with a 26% yield. The native protein is a monomer of 56.2 kDa that efficiently uses P6C (apparent Km 14 μM) and NAD+ (apparent Km 115 μM), but not NADP+ or other electron acceptors, as substrates. The enzyme activity was inhibited (by 66%) by its end product NADH at 0.1 mM concentration. It did not show activity towards pyrroline-5-carboxylate and was separated by Blue-Sepharose chromatography from pyrroline-5-carboxylate dehydrogenase, an enzyme involved in the catabolism of proline. P6C dehydrogenase reached maximal activity later than other early enzymes of the cephamycin pathway. The P6C dehydrogenase activity was decreased in ammonium (40 mM)-supplemented cultures, as was that of lysine 6-aminotransferase. P6C dehydrogenase activity was also found in other cephamycin C producers (Streptomyces cattleya and Nocardia lactamdurans) but not in actinomycetes that do not produce β-lactams, suggesting that it is an enzyme specific for cephamycin biosynthesis, involved in the second stage of the two-step conversion of lysine to α-aminoadipic acid.
Expression, purification and characterization of Arabidopsis thaliana acetohydroxyacid synthase
Authors: CHANG Alan K. , DUGGLEBY Ronald G. 
Published: August 2015

Acetohydroxyacid synthase (EC 4.1.3.18) is the enzyme that catalyses the first step in the synthesis of the branched-chain amino acids valine, leucine and isoleucine. The AHAS gene from Arabidopsis thaliana with part of the chloroplast transit sequence removed was cloned into the bacterial expression vector pT7-7 and expressed in the Escherichia coli strain BL21(DE3). The expressed enzyme was purified by an extensive procedure involving (NH4)2SO4 fractionation followed by hydrophobic and anion-exchange chromatography. The purified enzyme appears as a single band on SDS/PAGE with a molecular mass of about 61 kDa. On gel filtration the enzyme is a dimer, migrating as a single peak with molecular masses of 109 and 113 kDa in the absence and presence of FAD respectively. Ion spray MS analysis yielded a mass of 63864 Da. The enzyme has optimum activity in the pH range 6.5–8.5 and exhibits absolute dependence on the three cofactors FAD, Mg2+ and thiamine diphosphate for activity. It displays negatively co-operative kinetics with respect to pyruvate concentration. A model was derived to explain the non-hyperbolic substrate-saturation curve, involving interaction between the active sites of the dimer. The Km for the first active site was found to be 8.01±0.66 mM; the Km for the second active site could not be accurately determined but was estimated to be approx. 100 mM. The enzyme is insensitive to valine, leucine and isoleucine but is strongly inhibited by the sulphonylurea herbicide, chlorsulphuron, and the imidazolinone herbicide, imazapyr. Inhibition by both herbicides exhibits slow-binding kinetics, whereas chlorsulphuron also shows tight-binding inhibition.
Incorporation of copper into lysyl oxidase
Authors: KOSONEN Taru , URIU-HARE Janet Y. , CLEGG Michael S. , KEEN Carl L. , RUCKER Robert B. 
Published: August 2015

Lysyl oxidase is a copper-dependent enzyme involved in extracellular processing of collagens and elastin. Although it is known that copper is essential for the functional activity of the enzyme, there is little information on the incorporation of copper. In the present study we examined the insertion of copper into lysyl oxidase using 67Cu in cell-free transcription/translation assays and in normal skin fibroblast culture systems. When a full-length lysyl oxidase cDNA was used as a template for transcription/translation reactions in vitro, unprocessed prolysyl oxidase appeared to bind copper. To examine further the post-translational incorporation of copper into lysyl oxidase, confluent skin fibroblasts were incubated with inhibitors of protein synthesis (cycloheximide, 10 μg/ml), glycosylation (tunicamycin, 10 μg/ml), protein secretion (brefeldin A, 10 μg/ml) and prolysyl oxidase processing (procollagen C-peptidase inhibitor, 2.5 μg/ml) together with 300 μCi of carrier-free 67Cu. It was observed that protein synthesis was a prerequisite for copper incorporation, but inhibition of glycosylation by tunicamycin did not affect the secretion of 67Cu as lysyl oxidase. Brefeldin A inhibited the secretion of 67Cu-labelled lysyl oxidase by 46%, but the intracellular incorporation of copper into lysyl oxidase was not affected. In addition, the inhibition of the extracellular proteolytic processing of prolysyl oxidase to lysyl oxidase had minimal effects on the secretion of protein-bound 67Cu. Our results indicate that, similar to caeruloplasmin processing [Sato and Gitlin (1991) J. Biol. Chem. 266, 5128–5134], copper is inserted into prolysyl oxidase independently of glycosylation.
Binding of a burst-phase intermediate formed in the folding of denatured D-glyceraldehyde-3-phosphate dehydrogenase by chaperonin 60 and 8-anilino-1-naphthalenesulphonic acid
Authors: LI Xiao-Ling , LEI Xiang-Dong , CAI Hui , LI Jian , YANG Sheng-Li , WANG Chih-Chen , TSOU Chen-Lu 
Published: August 2015

Upon dilution, d-glyceraldehyde-3-phosphate dehydrogenase (GADPH) that has been fully inactivated, but only partially unfolded, in dilute guanidine hydrochloride (GuHCl) recovers activity completely. The fully unfolded enzyme, however, is re-activated only to a limited extent after dilution, and refolds rapidly in a burst phase to a partially folded intermediate characterized by increases in both the emission intensity of intrinsic fluorescence and binding to 8-anilino-1-naphthalenesulphonic acid (ANS). This intermediate aggregates with a time lag of a few minutes, and the aggregation can be suppressed completely by chaperonin 60 (GroEL). Stoichiometric analysis of the suppression of GAPDH re-activation by GroEL suggests that the tetradecameric GroEL binds to a dimeric GAPDH folding intermediate. This intermediate can be re-activated by ATP or ATP/chaperonin 10 (GroES) to an extent considerably greater than that obtained on spontaneous re-activation of the fully denatured enzyme upon dilution. Probing with a fluorescent derivative of NAD+ shows that this folding intermediate does not have a native conformation at the active site. The similar profiles of the effects of GroEL and ANS on the re-activation of GAPDH denatured by different concentrations of GuHCl suggest that GroEL and ANS recognize and bind to the same folding intermediate, which is similar to the relatively stable, partially unfolded, state of the enzyme denatured in 0.5–1.0 M GuHCl. However, the complexes of the intermediate with GroEL or ANS appear to be different, in that GroEL, but not ANS, suppresses aggregation and assists folding in the presence of ATP.
Insulin targeting to the regulated secretory pathway after fusion with green fluorescent protein and firefly luciferase
Authors: POULI Aristea E. , KENNEDY Helen J. , SCHOFIELD J. George , RUTTER Guy A. 
Published: August 2015

We have prepared recombinant cDNAs encoding chimaeras between human preproinsulin (sp.B.C.A., for B-, Connecting- and A-peptides) and a thermostable mutant of green fluorescent protein (GFPS65T, V163A, GFP*). The subcellular localization of the expressed chimaeras was monitored in living insulin-secreting INS-1 β-cells by laser scanning confocal microscopy. When GFP* was fused at the immediate N-terminus of the B-chain (sp.[GFP*].B.C.A.myc) two distinct patterns of fluorescence were apparent. In 1530/1740 cells examined, fluorescence was confined to a reticular, exclusively extranuclear structure, and closely co-localized with the endoplasmic reticulum marker, calreticulin. However, 210/1740 (12.1%) of cells displayed punctate fluorescence, which partially co-localized with the trans-Golgi network marker, TGN 38, and with the dense core secretory granule marker, phogrin. Since secretion of GFP* fluorescence into the medium could not readily be measured, we prepared a chimaera in which firefly luciferase was fused at the C-terminus of proinsulin (sp.B.C.A.myc.[Luc]). This chimaera displayed a distribution closely similar to that of sp.[GFP*].B.C.A.myc, but with a lower proportion (15/310, 4.8%) of the cells showing clear punctate distribution. At substimulatory glucose concentrations (3 mM) secretion of sp.B.C.A.myc.[Luc] could not be detected (rate of release into the medium identical with that of the cytosolic Renilla reniformis luciferase), indicating that the chimaera did not enter the constitutive secretory pathway. However, elevated (30 mM) glucose stimulated the release of the sp.B.C.A.myc.[Luc] luciferase chimaera, without a detectable effect on R. reniformis luciferase release. These data suggest that fusion of insulin, and the much larger photoproteins GFP* and luciferase, leads predominantly to misfolding and retention in the endoplasmic reticulum. However, the properly folded chimaeras are apparently still correctly targeted to the regulated, rather than the constitutive, secretory pathway. These chimaeras should therefore be valuable tools to monitor the exocytosis of insulin in real time.
Human cathepsin K cleaves native type I and II collagens at the N-terminal end of the triple helix
Authors: KAFIENAH Wa'el , BRÖMME Dieter , BUTTLE David J. , CROUCHER Lisa J. , HOLLANDER Anthony P. 
Published: August 2015

Cathepsin K (EC 3.4.22.38) is a recently described enzyme that has been shown to cleave type I collagen in its triple helix. The aim of this study was to determine if it also cleaves type II collagen in the triple helix and to identify the helical cleavage site(s) in types I and II collagens. Soluble human and bovine type II collagen, and rat type I collagen, were incubated with cathepsin K before the reaction was stopped with trans-epoxysuccinyl-l-leucylamido-(4-guanidino)butane (E-64). Analysis by SDS/PAGE of the collagen digests showed that optimal activity of cathepsin K against native type II collagen was between pH 5.0 and 5.5 and against denatured collagen between pH 4.0 and 7.0. The enzyme cleaved telopeptides as well as the α1(II) chains, generating multiple fragments in the range 90–120 kDa. The collagenolytic activity was not due to a contaminating metalloenzyme or serine proteinase as it was not inhibited by 1,10-phenanthroline, EDTA or 3,4-dichloroisocoumarin. Western blotting with anti-peptide antibodies to different regions of the α1(II) chain suggested that cathepsin K cleaved native α1(II) chains in the N-terminal region of the helical domain rather than at the well-defined collagenase cleavage site. This was confirmed by N-terminal sequencing of one of the fragments, revealing cleavage at a Gly-Lys bond, 58 residues from the N-terminus of the helical domain. By using a similar approach, cathepsin K was found to cleave native type I collagen close to the N-terminus of its triple helix. These results indicate that cathepsin K could have a role in the turnover of type II collagen, as well as type I collagen.