bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of ubiquitin and ubiquitin‐like‐protein isopeptidase activities
Authors: Nicholson Benjamin , Leach Craig A. , Goldenberg Seth J. , Francis Dana M. , Kodrasov Matthew P. , Tian Xufan , Shanks John , Sterner David E. , Bernal Alejandro , Mattern Michael R. , Wilkinson Keith D. , Butt Tauseef R. 
Published: April 2008

AbstractConjugation or deconjugation of ubiquitin (Ub) or ubiquitin‐like proteins (UBLs) to or from cellular proteins is a multifaceted and universal means of regulating cellular physiology, controlling the lifetime, localization, and activity of many critical proteins. Deconjugation of Ub or UBL from proteins is performed by a class of proteases called isopeptidases. Herein is described a readily quantifiable novel isopeptidase assay platform consisting of Ub or UBL fused to the reporter enzyme phospholipase A2 (PLA2). Isopeptidase activity releases PLA2, which cleaves its substrate, generating a signal that is linear with deubiquitylase (DUB) concentration and is able to discriminate DUB, deSUMOylase, deNEDDylase, and deISGylase activities. The power and sensitivity of the UBL‐PLA2 assay are demonstrated by its ability to differentiate the contrasting deISGylase and DUB activities of two coronavirus proteases: severe acute respiratory syndrome papain‐like protease (SARS‐CoV PLpro) and NL63 CoV papain‐like protease 2 (PLP2). Furthermore, direct comparisons with the current Ub‐7‐amino‐4‐methylcoumarin (Ub‐AMC) assay demonstrated that the Ub‐PLA2 assay is an effective tool for characterizing modulators of isopeptidase activity. This observation was expanded by profiling the inhibitory activity of the nonselective isopeptidase inhibitor NSC 632839 against DUBs and deSUMOylases. Taken together, these studies illustrate the utility of the reporter‐based approach to measuring isopeptidase activity.
Crystal structures of barley thioredoxin h isoforms HvTrxh1 and HvTrxh2 reveal features involved in protein recognition and possibly in discriminating the isoform specificity
Authors: Maeda Kenji , Hägglund Per , Finnie Christine , Svensson Birte , Henriksen Anette 
Published: April 2008

AbstractH‐type thioredoxins (Trxs) constitute a particularly large Trx sub‐group in higher plants. Here, the crystal structures are determined for the two barley Trx h isoforms, HvTrxh1 and HvTrxh2, in the partially radiation‐reduced state to resolutions of 1.7 Å, and for HvTrxh2 in the oxidized state to 2.0 Å. The two Trxs have a sequence identity of 51% and highly similar fold and active‐site architecture. Interestingly, the four independent molecules in the crystals of HvTrxh1 form two relatively large and essentially identical protein–protein interfaces. In each interface, a loop segment of one HvTrxh1 molecule is positioned along a shallow hydrophobic groove at the primary nucleophile Cys40 of another HvTrxh1 molecule. The association mode can serve as a model for the target protein recognition by Trx, as it brings the Met82 Cγ atom (γ position as a disulfide sulfur) of the bound loop segment in the proximity of the Cys40 thiol. The interaction involves three characteristic backbone–backbone hydrogen bonds in an antiparallel β‐sheet‐like arrangement, similar to the arrangement observed in the structure of an engineered, covalently bound complex between Trx and a substrate protein, as reported by Maeda et al. in an earlier paper. The occurrence of an intermolecular salt bridge between Glu80 of the bound loop segment and Arg101 near the hydrophobic groove suggests that charge complementarity plays a role in the specificity of Trx. In HvTrxh2, isoleucine corresponds to this arginine, which emphasizes the potential for specificity differences between the coexisting barley Trx isoforms.
Distinguishing the cross‐β spine arrangements in amyloid fibrils using FRET analysis
Authors: Deng Wei , Cao Aoneng , Lai Luhua 
Published: April 2008

AbstractThe recently published microcrystal structures of amyloid fibrils from small peptides greatly enhanced our understanding of the atomic‐level structure of the amyloid fibril. However, only a few amyloid fibrils can form microcrystals. The dansyl‐tryptophan fluorescence resonance energy transfer (FRET) pair was shown to be able to detect the inter‐peptide arrangement of the Transthyretin (105–115) amyloid fibril. In this study, we combined the known microcrystal structures with the corresponding FRET efficiencies to build a model for amyloid fibril structure classification. We found that fibrils with an antiparallel structural arrangement gave the largest FRET signal, those with a parallel arrangement gave the lowest FRET signal, and those with a mixed arrangement gave a moderate FRET signal. This confirms that the amyloid fibril structure patterns can be classified based on the FRET efficiency.
Autologous bone marrow cell infusion therapy for liver cirrhosis
Authors: Sakaida Isao 
Published: April 2008

AbstractThe plasticity of bone marrow cells (BMC) has been confirmed by autopsy results of female recipients of BMC from male donors. To establish new clinical therapies for patients with liver cirrhosis using autologous BMC, we developed a new in vivo murine model using green fluorescent protein (GFP) and repeated carbon tetrachloride (CCl4) injection. We found that BMC infused through the tail vein, efficiently repopulated cirrhotic liver tissue and, under the influence of persistent liver damage induced by carbon tetrachloride, differentiated into albumin‐producing hepatocytes. Moreover, such BMC infusions into mice with cirrhosis improved liver function and reduced mortality. The latter observation correlated with the strong expression of matrix metalloproteinases (MMP), particularly MMP‐9, and reduced hepatic fibrosis. The results from the ‘GFP/CCl4 model’ showed that cell therapy using autologous BMC has the potential to become an effective treatment for patients with liver failure due to advanced liver cirrhosis. This review summarizes previous findings plus these recent experimental results, as well as recent clinical trials of BMC transfusion into patients with end‐stage chronic liver disease.
Polaprezinc attenuates liver fibrosis in a mouse model of non‐alcoholic steatohepatitis
Authors: Sugino Haruko , Kumagai Naoki , Watanabe Sakiko , Toda Kyoko , Takeuchi Osamu , Tsunematsu Satoshi , Morinaga Shojiroh , Tsuchimoto Kanji 
Published: April 2008

AbstractBackground and Aim:  The effect of polaprezinc, a zinc‐carnosine chelate compound, on the development of non‐alcoholic steatohepatitis (NASH) was investigated in dietary methionine and choline deficient (MCD) mice.Methods:  Mice were fed the MCD diet with or without polaprezinc (2.2 g/kg diet) for 10 weeks. Liver histopathology, triglyceride and lipid peroxide levels, and the expression of genes linked to fibrosis were then assessed.Results:  MCD mice developed steatohepatitis accompanied by mild fibrosis with an increase in lipid peroxidation, hepatic stellate cell (HSC) activation, and the augmented mRNA expression of tumor necrosis factor‐α, transforming growth factor‐β1 and procollagen α1(I). The mRNA expression levels of matrix metalloproteinase (MMP)‐2 and tissue inhibitors of metalloproteinase (TIMP)‐1 and TIMP‐2 were also enhanced. Histopathologically, polaprezinc supplementation did not influence the development of steatosis but it apparently attenuated fibrosis. Polaprezinc slightly reduced lipid peroxidation and suppressed HSC activation as well as the mRNA expression of pro‐inflammatory cytokines. Polaprezinc affected the MCD diet‐enhanced expression of TIMP‐1 even when administered relatively late.Conclusion:  These results suggest that polaprezinc attenuates fibrosis in NASH by reducing inflammation and lipid peroxidation and, during a later phase, promoting fibrolysis via the inhibition of TIMP expression in the liver. Further investigation is required to clarify the clinical efficacy of polaprezinc in patients with NASH.
Optimal systemic hemodynamic stability for successful clinical outcomes after adult living‐donor liver transplantation: Prospective observational study
Authors: Hori Tomohide , Yagi Shintaro , Iida Taku , Taniguchi Kentaro , Yamagiwa Kentaro , Yamamoto Chiduru , Hasegawa Takashi , Yamakado Koichiro , Kato Takuma , Saito Kanako , Wang Linan , Torii Mie , Hori Yukinobu , Takeda Kan , Maruyama Kazuo , Uemoto Shinji 
Published: April 2008

AbstractBackground and Aim:  Most living‐donor liver transplantation (LDLT) recipients show characteristic systemic hemodynamics due to liver cirrhosis, and systemic hemodynamics after LDLT influenced postoperative graft function corresponding to outcomes. However, identities of optimal systemic hemodynamics for excellent outcomes and precise parameters for clinical strategy remain unclear.Methods:  Therefore, we performed prospective study in adult LDLT recipients from 2003. Hemodynamic parameters were prospectively recorded, and were analyzed in 40 recipients classified into three groups: cirrhotic (group I‐C) or non‐cirrhotic recipients (group I‐NC) with good outcomes, and cirrhotic recipients (group II‐C) without good outcomes.Results:  Group I‐C retained characteristic hyperdynamics even after LDLT. However, absolute values of parameters revealed no significant differences between groups I‐C and II‐C, because group II‐C also tended to show hyperdynamics. It is suggested that successful outcomes in cirrhotic recipients require maintenance of optimal hyperdynamic stability after LDLT, because cirrhotic vascular alterations still occurred. Because hemodynamic behaviors were different between groups I‐C and I‐NC, absolute values were also significantly different even in these successful two groups. Thus, absolute values themselves were not necessarily satisfactory for accurate evaluation of optimal hemodynamic stability. Cirrhotic hyperdynamics are symbolized in large blood volume (BV) circulated by high cardiac output (CO); therefore, we standardized CO against BV. CO/BV was significantly different between groups I‐C and II‐C, reflecting subtle variability of hyperdynamics in groups II‐C, and was interestingly constant in the two successful groups. Therefore, CO/BV reliably evaluated optimal hemodynamic stability after LDLT, and accurately predicted outcomes.Conclusion:  Identification of inappropriate hemodynamics after LDLT is advantageous to further improve LDLT outcomes.
Des‐γ‐carboxyprothrombin, α‐fetoprotein and AFP‐L3 in patients with chronic hepatitis, cirrhosis and hepatocellular carcinoma
Authors: Durazo Francisco A , Blatt Lawrence M , Corey William G , Lin Jiing‐Huey , Han Steven , Saab Sammy , Busuttil Ronald W , Tong Myron J 
Published: April 2008

AbstractBackground and Aim:  Hepatocellular carcinoma (HCC) is a common complication in patients with chronic viral hepatitis. Detection of HCC at an early stage is critical for a favorable clinical outcome. The study aim was to: (i) compare the levels of des‐γ‐carboxyprothrombin (DCP), α‐fetoprotein (AFP) and AFP‐L3 in HCC patients and in chronic viral hepatitis patients without HCC; (ii) define the level of each tumor marker with the best sensitivity and specificity for HCC diagnosis; and (iii) to correlate the levels of these markers with respect to size and tumor burden.Methods:  Two hundred and forty patients with either hepatitis B virus (HBV) or hepatitis C virus (HCV) infection were studied. These included 144 with HCC, 47 with chronic hepatitis (fibrosis stage I–III on liver biopsy) and 49 with cirrhosis.Results:  Levels of DCP, AFP and AFP L‐3 were significantly higher in patients with HCC than in those without HCC (P ≤ 0.0001). Receiver–operating curves (ROC) indicated that the cut‐off value with the best sensitivity and specificity for each test was ≥84 mAU/mL for DCP, ≥25 ng/mL for AFP and ≥10% for AFP‐L3. The sensitivity, specificity and positive predictive value (PPV) for DCP was 87%, 85% and 86.8%, for AFP 69%, 87% and 69.8%, and for AFP‐L3 56%, 90% and 56.1%, respectively. DCP levels were below the ROC cut‐off in all patients without HCC. In patients with single lesions, there was a direct correlation of DCP to tumor size. High levels of AFP correlated with diffuse type of HCC. All three markers were significantly elevated in the presence of metastatic HCC. No advantage was observed by combining two or three markers for HCC diagnosis.Conclusion:  DCP had the highest sensitivity and PPV for HCC diagnosis, had a direct correlation with tumor size, and was not elevated in any patients without HCC. DCP should be used as the main serum test for HCC detection.
Pegylated α‐interferon‐2a plus ribavirin compared with pegylated α‐interferon‐2b plus ribavirin for initial treatment of chronic hepatitis C virus: Prospective, non‐randomized study
Authors: Escudero Amparo , Rodríguez Felicidad , Serra Miguel A , Del Olmo Juan A , Montes Francisco , Rodrigo José M 
Published: April 2008

AbstractBackground and Aim:  We assessed whether the two regimens of pegylated α‐interferon‐2b (PEG‐IFN‐α2b) plus ribavirin and pegylated α‐interferon‐2a (PEG‐IFN‐α2a) plus ribavirin showed differences in terms of sustained virological response, withdrawal due to side‐effects and dose adjustment requirements in the treatment of naive chronic hepatitis C virus (HCV) patients.Methods:  A prospective non‐randomized, open‐label comparison was made of naive HCV‐infected patients undergoing standard 24‐ or 48‐week treatment with two PEG‐IFN combined with weight‐based dosing regimen of ribavirin (PEG‐IFN‐α2a/ribavirin, n = 91; PEG‐IFN‐α2b/ribavirin, n = 92).Results:  Sustained virological response was similar in PEG‐IFN‐α2a and PEG‐IFN‐α2b (65.9% vs 62%, P = 0.64), without differences according to genotype. In 117 patients with HCV genotype 1, the corresponding rates were 50.8% versus 46.6% (P = 0.713). Rapid virological response at 4 weeks, early virological response at 12 weeks and transient virological response were also similar. In the multivariate analysis, HCV genotype (odds ratio [OR] = 0.076, 95% confidence interval [CI] 0.029–0.198, P = 0.000) and presence of steatosis in the liver biopsy (OR = 2.799, 95% CI 1.362–5.755, P = 0.005) were significantly associated with response to antiviral therapy. The rate of withdrawals due to treatment‐related adverse events was 13.2% in the group of PEG‐IFN‐α2a and 10.9% in the group of PEG‐IFN‐α2b. Dose modification of PEG‐IFN was necessary in eight patients given PEG‐IFN‐α2a and in seven given PEG‐IFN‐α2b.Conclusion:  The two PEG‐IFN plus ribavirin have comparable anti‐HCV activity as shown by similar percentages of patients with sustained virological response.
ATP‐binding cassette transporter A7 regulates processing of amyloid precursor protein in vitro
Authors: Chan Sharon L. , Kim Woojin Scott , Kwok John B. , Hill Andrew F. , Cappai Roberto , Rye Kerry‐Anne , Garner Brett 
Published: April 2008

AbstractATP‐binding cassette transporter A7 (ABCA7) is expressed in the brain and, like its closest homolog ABCA1, belongs to the ABCA subfamily of full‐length ABC transporters. ABCA1 promotes cellular cholesterol efflux to lipid‐free apolipoprotein acceptors and also inhibits the production of neurotoxic β‐amyloid (Aβ) peptides in vitro. The potential functions of ABCA7 in the brain are unknown. This study investigated the ability of ABCA7 to regulate cholesterol efflux to extracellular apolipoprotein acceptors and to modulate Aβ production. The transient expression of ABCA7 in human embryonic kidney cells significantly stimulated cholesterol efflux (fourfold) to apolipoprotein E (apoE) discoidal lipid complexes but not to lipid‐free apoE or apoA‐I. ABCA7 also significantly inhibited Aβ secretion from Chinese hamster ovary cells stably expressing human amyloid precursor protein (APP) or APP containing the Swedish K670M671→N670L671 mutations when compared with mock‐transfected cells. Studies with fluorogenic substrates indicated that ABCA7 had no impact on α‐, β‐, or γ‐secretase activities. Live cell imaging of Chinese hamster ovary cells expressing APP‐GFP indicated an apparent retention of APP in a perinuclear location in ABCA7 co‐transfected cells. These studies indicate that ABCA7 has the capacity to stimulate cellular cholesterol efflux to apoE discs and regulate APP processing resulting in an inhibition of Aβ production.
Zinc binding site in PICK1 is dominantly located at the CPC motif of its PDZ domain
Authors: Shi Yawei , Zhang Lei , Yuan Jingming , Xiao Hong , Yang Xiuqing , Niu Lixi 
Published: April 2008

AbstractPICK1 (protein interacting with Ckinase 1) containing a PDZ domain, a BAR domain, and two short acidic regions is as an adaptor protein that plays an important role in α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionic acid receptor trafficking, cell morphology and migration, as well as in some diseases such as cancer, schizophrenia and pain. To better understand the physiological function of PICK1, we expressed the recombinant PICK1 and its truncated mutants in E.coli, and measured their zinc binding properties by fluorescence and competition assay. It is shown that PICK1 has one Zn2+‐binding site. The Zn2+‐binding properties of PICK1 are not appreciably affected after the removal of BARC domain (involving BAR domain and C‐terminal acidic region). Deleting the N‐terminal acidic region of NPDZ domain (involving PDZ domain and N‐terminal acidic region) in PICK1 impairs its Zn2+‐binding capacity.The mutation of the CPC (Cys‐Pro‐Cys) motif in the PDZ domain of PICK1 abolishes the ability of Zn2+‐binding. In addition, Zn2+ can enhance the lipid‐binding ability of PDZ domain as observed in both protein‐lipid overlay assay and fluorescence analysis. The results presented in this report suggested that Zn2+ plays a regulatory role in the trafficking of PICK1 from the cytoplasm to cell membrane.
Inhibitory effects of aripiprazole on interferon‐γ‐induced microglial activation via intracellular Ca2+ regulation in vitro
Authors: Kato Takahiro , Mizoguchi Yoshito , Monji Akira , Horikawa Hideki , Suzuki Satoshi O. , Seki Yoshihiro , Iwaki Toru , Hashioka Sadayuki , Kanba Shigenobu 
Published: April 2008

AbstractThe activation of the inflammatory/immunological response system is suggested to be related to the pathophysiology of schizophrenia. Aripiprazole is a novel atypical antipsychotic, which is a high‐affinity dopamine D2 receptor partial agonist. Atypical antipsychotics, all of which have dopamine D2 receptor antagonism, have recently reported to have significantly inhibitory effects on interferon (IFN)‐γ‐induced microglial activation in vitro. In the present study, we investigated whether or not aripiprazole also has anti‐inflammatory effect on IFN‐γ‐induced microglial activation. Not quinpirole, dopamine D2 full agonist, but aripiprazole significantly inhibited the generation of nitric oxide (NO) and tumor necrosis factor (TNF)‐α from IFN‐γ‐activated microglia and suppressed the IFN‐γ‐induced elevation of intracellular Ca2+ concentrations ([Ca2+]i) in murine microglial cells. Increased [Ca2+]i has been reported to be required, but by itself not sufficient, for the release of NO and certain cytokines. As a result, we can speculate that aripiprazole may inhibit IFN‐γ‐induced microglial activation through the suppression of IFN‐γ‐induced elevation of [Ca2+]i in microglia. Our results demonstrated that not only antipsychotics which have dopamine D2 receptor antagonism but also aripiprazole have anti‐inflammatory effects via the inhibition of microglial activation. Antipsychotics may therefore have a potentially useful therapeutic effect on patients with schizophrenia by reducing the microglial inflammatory reactions.
Expression of mRNA for specific fibroblast growth factors associates with that of the myogenic markers MyoD and proliferating cell nuclear antigen in regenerating and overloaded rat plantaris muscle
Authors: Tanaka Y. , Yamaguchi A. , Fujikawa T. , Sakuma K. , Morita I. , Ishii K. 
Published: April 2008

AbstractAim:  To examine the relations between specific fibroblast growth factors (FGFs) and satellite cell activation during muscle regeneration and hypertrophy in vivo, we measured mRNA expression of FGFs and myogenic markers in rat plantaris muscle after bupivacaine administration and synergist ablation.Methods:  mRNA levels for MyoD, myogenin, proliferating cell nuclear antigen (PCNA), p21, M‐cadherin, Pax7, FGF‐1, FGF‐2, FGF‐3, FGF‐4, FGF‐5, FGF‐6, FGF‐7, FGF‐8 and hepatocyte growth factor (HGF) were measured continually for up to 72 h after bupivacaine administration and synergist ablation. FGF‐5, FGF‐7 and HGF proteins were immunostained at 72 h after bupivacaine administration.Results:  MyoD and PCNA mRNAs started increasing 24 h after bupivacaine administration. Myogenin, p21, M‐cadherin and Pax7 mRNAs started to increase after 48 and 72 h. After synergist ablation, MyoD, PCNA, M‐cadherin and Pax7 mRNAs had increased at 24 and 48 h, and myogenin and p21 mRNAs at 12 and 24 h. FGF‐1, FGF‐7 and HGF mRNAs after the treatments started to increase at the same time as MyoD and PCNA mRNAs. FGF‐5 was expressed at the same time as MyoD and PCNA mRNAs after bupivacaine administration but did not after the ablation. FGF‐2, FGF‐3, FGF‐4, FGF‐6 and FGF‐8 mRNAs were not associated with the expression of the myogenic markers. FGF‐7 and HGF proteins were expressed in immature muscle fibre nuclei and the extracellular matrix, but FGF‐5 protein was preferentially expressed in extracellular matrix.Conclusion:  These results indicate that FGF‐1, FGF‐7 and HGF are associated with specific myogenic marker expression during muscle regeneration and hypertrophy.
Characterization of the Pattern of α
s1
- and β-Casein Breakdown and Release of a Bioactive Peptide by a Cell Envelope Proteinase from
Lactobacillus delbrueckii
subsp.
lactis
CRL 581
Authors: Hebert Elvira María , Mamone Gianfranco , Picariello Gianluca , Raya Raúl R. , Savoy Graciela , Ferranti Pasquale , Addeo Francesco 
Published: April 2008

ABSTRACT

The cell envelope-associated proteinases (CEPs) of the lactobacilli have key roles in bacterial nutrition and contribute to the development of the organoleptic properties of fermented milk products as well, as they can release bioactive health-beneficial peptides from milk proteins. The influence of the peptide supply, carbohydrate source, and osmolites on the CEP activity of the cheese starter
Lactobacillus delbrueckii
subsp.
lactis
CRL 581 was investigated. The CEP activity levels were controlled by the peptide content of the growth medium. The maximum activity was observed in a basal minimal defined medium, whereas in the presence of Casitone, Casamino Acids, or yeast extract, the synthesis of CEP was inhibited 99-, 70-, and 68-fold, respectively. The addition of specific di- or tripeptides containing branched-chain amino acids, such as leucylleucine, prolylleucine, leucylglycylglycine, or leucylproline, to the growth medium negatively affected CEP activity, whereas dipeptides without branched-chain amino acids had no effect on the enzyme's production. The carbon source and osmolites did not affect CEP activity. The CEP of
L. delbrueckii
subsp.
lactis
CRL 581 exhibited a mixed-type CEP
I/III
variant caseinolytic specificity. Mass-spectrometric screening of the main peptide peaks isolated by reverse-phase high-pressure liquid chromatography allowed the identification of 33 and 32 peptides in the α
s1
- and β-casein hydrolysates, respectively. By characterizing the peptide sequence in these hydrolysates, a pattern of α
s1
- and β-casein breakdown was defined and is reported herein, this being the first report for a CEP of
L. delbrueckii
subsp.
lactis
. In this pattern, a series of potentially bioactive peptides (antihypertensive and phosphopeptides) which are encrypted within the precursor protein could be visualized.