bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of 3′-Phosphate RNA Ligase Paralogs RtcB1, RtcB2, and RtcB3 from Myxococcus xanthus Highlights DNA and RNA 5′-Phosphate Capping Activity of RtcB3
Authors: Maughan William P. , Shuman Stewart 
Published: September 2015

ABSTRACT

Escherichia coli
RtcB exemplifies a family of GTP-dependent RNA repair/splicing enzymes that join 3′-PO
4
ends to 5′-OH ends via stable RtcB-(histidinyl-
N
)-GMP and transient RNA
3′
pp
5′
G intermediates.
E. coli
RtcB also transfers GMP to a DNA 3′-PO
4
end to form a stable “capped” product, DNA
3′
pp
5′
G. RtcB homologs are found in a multitude of bacterial proteomes, and many bacteria have genes encoding two or more RtcB paralogs; an extreme example is
Myxococcus xanthus
, which has six RtcBs. In this study, we purified, characterized, and compared the biochemical activities of three
M. xanthus
RtcB paralogs. We found that
M. xanthus
RtcB1 resembles
E. coli
RtcB in its ability to perform intra- and intermolecular sealing of a
HO
RNAp substrate and capping of a DNA 3′-PO
4
end.
M. xanthus
RtcB2 can splice
HO
RNAp but has 5-fold-lower RNA ligase specific activity than RtcB1. In contrast,
M. xanthus
RtcB3 is distinctively feeble at ligating the
HO
RNAp substrate, although it readily caps a DNA 3′-PO
4
end. The novelty of
M. xanthus
RtcB3 is its capacity to cap DNA and RNA 5′-PO
4
ends to form GppDNA and GppRNA products, respectively. As such, RtcB3 joins a growing list of enzymes (including RNA 3′-phosphate cyclase RtcA and thermophilic ATP-dependent RNA ligases) that can cap either end of a polynucleotide substrate. GppDNA formed by RtcB3 can be decapped to pDNA by the DNA repair enzyme aprataxin.

IMPORTANCE
RtcB enzymes comprise a widely distributed family of RNA 3′-PO
4
ligases distinguished by their formation of 3′-GMP-capped RNAppG and/or DNAppG polynucleotides. The mechanism and biochemical repertoire of
E. coli
RtcB are well studied, but it is unclear whether its properties apply to the many bacteria that have genes encoding multiple RtcB paralogs. A comparison of the biochemical activities of three
M. xanthus
paralogs, RtcB1, RtcB2, and RtcB3, shows that not all RtcBs are created equal. The standout findings concern RtcB3, which is (i) inactive as an RNA 3′-PO
4
ligase but adept at capping a DNA 3′-PO
4
end and (ii) able to cap DNA and RNA 5′-PO
4
ends to form GppDNA and GppRNA, respectively. The GppDNA and GppRNA capping reactions are novel nucleic acid modifications.
Association with PAK2 Enables Functional Interactions of Lentiviral Nef Proteins with the Exocyst Complex
Authors: Imle Andrea , Abraham Libin , Tsopoulidis Nikolaos , Hoflack Bernard , Saksela Kalle , Fackler Oliver T. 
Published: September 2015

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) Nef enhances virus replication and contributes to immune evasion
in vivo
, but the underlying molecular mechanisms remain incompletely defined. Nef interferes with host cell actin dynamics to restrict T lymphocyte responses to chemokine stimulation and T cell receptor engagement. This relies on the assembly of a labile multiprotein complex including the host kinase PAK2 that Nef usurps to phosphorylate and inactivate the actin-severing factor cofilin. Components of the exocyst complex (EXOC), an octameric protein complex involved in vesicular transport and actin remodeling, were recently reported to interact with Nef via the same molecular surface that mediates PAK2 association. Exploring the functional relevance of EXOC in Nef-PAK2 complex assembly/function, we found Nef-EXOC interactions to be specifically mediated by the PAK2 interface of Nef, to occur in infected human T lymphocytes, and to be conserved among lentiviral Nef proteins. In turn, EXOC was dispensable for direct downstream effector functions of Nef-associated PAK2. Surprisingly, PAK2 was essential for Nef-EXOC association, which required a functional Rac1/Cdc42 binding site but not the catalytic activity of PAK2. EXOC was dispensable for Nef functions in vesicular transport but critical for inhibition of actin remodeling and proximal signaling upon T cell receptor engagement. Thus, Nef exploits PAK2 in a stepwise mechanism in which its kinase activity cooperates with an adaptor function for EXOC to inhibit host cell actin dynamics.

IMPORTANCE
Human immunodeficiency virus type 1 (HIV-1) Nef contributes to AIDS pathogenesis, but the underlying molecular mechanisms remain incompletely understood. An important aspect of Nef function is to facilitate virus replication by disrupting T lymphocyte actin dynamics in response to stimulation via its association with the host cell kinase PAK2. We report here that the molecular surface of Nef for PAK2 association also mediates interaction of Nef with EXOC and establish that PAK2 provides an essential adaptor function for the subsequent formation of Nef-EXOC complexes. PAK2 and EXOC specifically cooperate in the inhibition of actin dynamics and proximal signaling induced by T cell receptor engagement by Nef. These results establish EXOC as a functionally relevant Nef interaction partner, emphasize the suitability of the PAK2 interaction surface for future therapeutic interference with Nef function, and show that such strategies need to target activity-independent PAK2 functions.
N
-Acetylglucosamine-Induced Cell Death in Candida albicans and Its Implications for Adaptive Mechanisms of Nutrient Sensing in Yeasts
Authors: Du Han , Guan Guobo , Li Xiaoling , Gulati Megha , Tao Li , Cao Chengjun , Johnson Alexander D. , Nobile Clarissa J. , Huang Guanghua 
Published: September 2015

ABSTRACT

Single-celled organisms have different strategies to sense and utilize nutrients in their ever-changing environments. The opportunistic fungal pathogen
Candida albicans
is a common member of the human microbiota, especially that of the gastrointestinal (GI) tract. An important question concerns how
C. albicans
gained a competitive advantage over other microbes to become a successful commensal and opportunistic pathogen. Here, we report that
C. albicans
uses
N
-acetylglucosamine (GlcNAc), an abundant carbon source present in the GI tract, as a signal for nutrient availability. When placed in water,
C. albicans
cells normally enter the G
0
phase and remain viable for weeks. However, they quickly lose viability when cultured in water containing only GlcNAc. We term this phenomenon GlcNAc-induced cell death (GICD). GlcNAc triggers the upregulation of ribosomal biogenesis genes, alterations of mitochondrial metabolism, and the accumulation of reactive oxygen species (ROS), followed by rapid cell death via both apoptotic and necrotic mechanisms. Multiple pathways, including the conserved cyclic AMP (cAMP) signaling and GlcNAc catabolic pathways, are involved in GICD. GlcNAc acts as a signaling molecule to regulate multiple cellular programs in a coordinated manner and therefore maximizes the efficiency of nutrient use. This adaptive behavior allows
C. albicans
’ more efficient colonization of the gut.

IMPORTANCE
The ability to rapidly and appropriately respond to nutrients in the environment is crucial to free-living microorganisms. To maximize the use of available nutrients, microorganisms often use a limiting nutritional component as a signal to coordinate multiple biological processes. The human fungal pathogen
Candida albicans
uses
N
-acetylglucosamine (GlcNAc) as a signal for the availability of external nutrient resources. GlcNAc induces rapid cell death in
C. albicans
due to the constitutive activation of oxidative metabolism and accumulation of reactive oxygen species (ROS), and multiple pathways are involved in its regulation. This study sheds light on the mechanisms of niche specialization of pathogenic fungi and raises the possibility that this cell death pathway could be an unexplored therapeutic target.
Factors related to previous tuberculosis treatment of patients with multidrug-resistant tuberculosis in Bangladesh
Authors: Rifat Mahfuza , Hall John , Oldmeadow Christopher , Husain Ashaque , Hinderaker Sven Gudmund , Milton Abul Hasnat 
Published: September 2015

ObjectivePrevious tuberculosis (TB) treatment status is an established risk factor for multidrug-resistant TB (MDR-TB). This study explores which factors related to previous TB treatment may lead to the development of multidrug resistant in Bangladesh.DesignWe previously conducted a large case–control study to identify risk factors for developing MDR-TB in Bangladesh. Patients who had a history of previous TB treatment, either MDR-TB or non-MDR-TB, were interviewed about their previous treatment episode. This study restricts analysis to the strata of patients who have been previously treated for TB. Information was collected through face-to-face interviews and record reviews. Unadjusted and multivariable logistic regression was used for data analysis.SettingCentral-level, district-level and subdistrict-level hospitals in rural and urban Bangladesh.ResultsThe strata of previously treated patients include a total of 293 patients (245 current MDR-TB; 48 non-MDR-TB). Overall, 54% of patients received previous TB treatment more than once, and all of these patients were multidrug resistant. Patients with MDR-TB were more likely to have experienced the following factors: incomplete treatment (OR 4.3; 95% CI 1.7 to 10.6), adverse reactions due to TB treatment (OR 8.2; 95% CI 3.2 to 20.7), hospitalisation for symptoms associated with TB (OR 16.9; CI 1.8 to 156.2), DOTS (directly observed treatment, short-course) centre as treatment unit (OR 6.4; CI 1.8 to 22.8), supervised treatment (OR 3.8; CI 1.6 to 9.5); time-to-treatment centre (OR 0.984; CI 0.974 to 0.993).ConclusionsIncomplete treatment, hospitalisation for TB treatment and adverse reaction are the factors related to previous TB treatment of patients with MDR-TB. Although the presence of supervised treatment (DOT), less time-to-treatment centres and being treated in DOTS centres were relatively higher among the patients with MDR-TB compared with patients without MDR-TB, these findings include information of their most recent TB treatment episode only. Most (64.5%) of the patients with MDR-TB had received TB treatment more than once.
A retrospective pilot study of correlation of cerebral augmentation effects of external counterpulsation with functional outcome after acute ischaemic stroke
Authors: Xiong Li , Lin Wenhua , Han Jinghao , Chen Xiangyan , Leung Thomas Wai Hong , Soo Yannie Oi Yan , Wong Lawrence Ka Sing 
Published: September 2015

ObjectiveExternal counterpulsation (ECP) is a non-invasive method used to augment cerebral blood flow of patients with ischaemic stroke via induced hypertension. We aimed to explore the correlation between the cerebral blood flow augmentation effects induced by ECP and clinical outcome after acute ischaemic stroke.MethodsWe retrospectively analysed our ECP registry of patients with ischaemic stroke who were enrolled within 7 days after stroke onset. Bilateral middle cerebral arteries of patients were monitored using transcranial Doppler (TCD). Flow velocity changes before, during and after ECP were, respectively, recorded for 3 min. The cerebral augmentation index (CAI) was the increase in percentage of the middle cerebral artery mean flow velocity during ECP compared with baseline. TCD data were analysed based on the side ipsilateral or contralateral to the infarct. The modified Rankin Scale (mRS) (good outcome: mRS 0∼2; poor outcome: mRS 3∼6) was evaluated 6 months after the index stroke.Results72 patients were included (mean age, 63.8±10.7 years; 87.5% males). At month 6 after stroke onset, univariate analysis showed that the National Institutes of Health Stroke Scale at recruitment was significantly higher and ECP therapy duration was longer in the poor outcome group, while the ipsilateral CAI was significantly lower in the good outcome group than that in the poor outcome group (3.71±4.94 vs 7.73±7.66, p=0.044). Multivariate logistic regression showed that ipsilateral CAI was independently correlated with an unfavourable functional outcome after adjusting for confounding factors.ConclusionsThe higher degree of cerebral blood flow velocity augmentation on the side ipsilateral to the infarct induced by ECP is independently correlated with an unfavourable functional outcome after acute ischaemic stroke.
Pre-trial inter-laboratory analytical validation of the FOCUS4 personalised therapy trial
Authors: Richman Susan D , Adams Richard , Quirke Phil , Butler Rachel , Hemmings Gemma , Chambers Phil , Roberts Helen , James Michelle D , Wozniak Sue , Bathia Riya , Pugh Cheryl , Maughan Timothy , Jasani Bharat 
Published: September 2015

IntroductionMolecular characterisation of tumours is increasing personalisation of cancer therapy, tailored to an individual and their cancer. FOCUS4 is a molecularly stratified clinical trial for patients with advanced colorectal cancer. During an initial 16-week period of standard first-line chemotherapy, tumour tissue will undergo several molecular assays, with the results used for cohort allocation, then randomisation. Laboratories in Leeds and Cardiff will perform the molecular testing. The results of a rigorous pre-trial inter-laboratory analytical validation are presented and discussed.MethodsWales Cancer Bank supplied FFPE tumour blocks from 97 mCRC patients with consent for use in further research. Both laboratories processed each sample according to an agreed definitive FOCUS4 laboratory protocol, reporting results directly to the MRC Trial Management Group for independent cross-referencing.ResultsPyrosequencing analysis of mutation status atKRAScodons12/13/61/146,NRAScodons12/13/61,BRAFcodon600 andPIK3CAcodons542/545/546/1047, generated highly concordant results. Two samples gave discrepant results; in one aPIK3CAmutation was detected only in Leeds, and in the other, aPIK3CAmutation was only detected in Cardiff. pTEN and mismatch repair (MMR) protein expression was assessed by immunohistochemistry (IHC) resulting in 6/97 discordant results for pTEN and 5/388 for MMR, resolved upon joint review. Tumour heterogeneity was likely responsible for pyrosequencing discrepancies. The presence of signet-ring cells, necrosis, mucin, edge-effects and over-counterstaining influenced IHC discrepancies.ConclusionsPre-trial assay analytical validation is essential to ensure appropriate selection of patients for targeted therapies. This is feasible for both mutation testing and immunohistochemical assays and must be built into the workup of such trials.Trial registration numberISRCTN90061564.
Significantly reduced lymphadenopathy, salivary gland infiltrates and proteinuria in MRL-lpr/lprmice treated with ultrasoluble curcumin/turmeric: increased survival with curcumin treatment
Authors: Kurien Biji T , Harris Valerie M , Quadri Syed M S , Coutinho-de Souza Patricia , Cavett Joshua , Moyer Amanda , Ittiq Bilal , Metcalf Angela , Ramji Husayn F , Truong Dat , Kumar Ramesh , Koelsch Kristi A , Centola Mike , Payne Adam , Danda Debashish , Scofield R Hal 
Published: September 2015

ObjectivesCommercial curcumin (CU), derived from food spice turmeric (TU), has been widely studied as a potential therapeutic for a variety of oncological and inflammatory conditions. Lack of solubility/bioavailability has hindered curcumin's therapeutic efficacy in human diseases. We have solubilised curcumin in water applying heat/pressure, obtaining up to 35-fold increase in solubility (ultrasoluble curcumin (UsC)). We hypothesised that UsC or ultrasoluble turmeric (UsT) will ameliorate systemic lupus erythematosus (SLE) and Sjögren's syndrome (SS)-like disease in MRL-lpr/lprmice.MethodsEighteen female MRL-lpr/lpr(6 weeks old) and 18 female MRL-MpJ mice (6 weeks old) were used. Female MRL-lpr/lprmice develop lupus-like disease at the 10th week and die at an average age of 17 weeks. MRL-MpJ mice develop lupus-like disease around 47 weeks and typically die at 73 weeks. Six mice of each strain received autoclaved water only (lpr-water or MpJ-water group), UsC (lpr-CU or MpJ-CU group) or UsT (lpr-TU or MpJ-TU group) in the water bottle.ResultsUsC or UsT ameliorates SLE in the MRL-lpr/lprmice by significantly reducing lymphoproliferation, proteinuria, lesions (tail) and autoantibodies.lpr-CU group had a 20% survival advantage overlpr-water group. However,lpr-TU group lived an average of 16 days shorter thanlpr-water group due to complications unrelated to lupus-like illness. CU/TU treatment inhibited lymphadenopathy significantly compared withlpr-water group (p=0.03 and p=0.02, respectively) by induction of apoptosis. Average lymph node weights were 2606±1147, 742±331 and 385±68 mg, respectively, forlpr-water,lpr-CU andlpr-TU mice. Transferase dUTP nick end labelling assay showed that lymphocytes in lymph nodes oflpr-CU andlpr-TU mice underwent apoptosis. Significantly reduced cellular infiltration of the salivary glands in thelpr-TU group compared withthe lpr-water group, and a trend towards reduced kidney damage was observed in thelpr-CU andlpr-TU groups.ConclusionsThese studies show that UsC/UsT could prove useful as a therapeutic intervention in SLE/SS.
Complete Remissions of Adult T-cell Leukemia with Anti-CD25 Recombinant Immunotoxin LMB-2 and Chemotherapy to Block Immunogenicity
Authors: Kreitman Robert J. , Stetler-Stevenson Maryalice , Jaffe Elaine S. , Conlon Kevin C. , Steinberg Seth M. , Wilson Wyndham , Waldmann Thomas A. , Pastan Ira 
Published: September 2015

Abstract
Purpose: Adult T-cell leukemia (ATL) is usually CD25+ and rapidly fatal. Anti-CD25 recombinant immunotoxin LMB-2 had phase I activity limited by immunogenicity and rapid growth. To prevent antidrug antibodies and leukemic progression between cycles, a phase II trial was performed with LMB-2 after cyclophosphamide and fludarabine.
Experimental Design: ATL patients received cyclophosphamide and fludarabine days 1 to 3 and 2 weeks later began up to 6 cycles at 3-week intervals of cyclophosphamide and fludarabine days 1 to 3 followed by LMB-2 30–40 μg/kg i.v. days 3, 5, and 7. Three different dose levels of cyclophosphamide and fludarabine were used, 20+200 (n = 3), 25+250 (n = 12), and 30+300 mg/m2 (n = 2).
Results: Of 17 patients enrolled and treated with fludarabine and cyclophosphamide for cycle-1, 15 received subsequent cycle(s) containing LMB-2 and were therefore evaluable for response. Lack of antibody formation permitted retreatment in most patients. Of 10 evaluable leukemic patients receiving 25+250 or 30+300 mg/m2 of fludarabine and cyclophosphamide, 6 (60%) achieved complete remission (CR) and 2 (20%) partial remission (PR), and all 5 with &gt;25% leukemic cells achieved CR. No responses were achieved in 5 with lymphomatous ATL or lower fludarabine and cyclophosphamide doses. Median CR duration for the 6 CRs was 40 weeks. One is without detectable ATL at 47 months. Toxicity was mostly attributable to fludarabine and cyclophosphamide. Capillary leak from LMB-2 was non-dose limiting. One patient in CR died of a preexisting infection.
Conclusions: LMB-2, administered with fludarabine and cyclophosphamide to prevent antidrug antibodies and rapid intercycle progression, is highly effective in achieving CR in leukemia ATL. Fludarabine and cyclophosphamide dose/schedule is important for safety and efficacy in this high-risk population. Clin Cancer Res; 22(2); 310–8. ©2015 AACR.
Targeting FGFR Pathway in Human Hepatocellular Carcinoma: Expressing pFGFR and pMET for Antitumor Activity
Authors: Jo Jae-Cheol , Choi Eun Kyoung , Shin Jae-Sik , Moon Jai-Hee , Hong Seung-Woo , Lee Ha-Reum , Kim Seung-Mi , Jung Soo-A , Lee Dae-Hee , Jung Seang Hwan , Lee Sun-Hye , Kim Jeong Eun , Kim Kyu-pyo , Hong Yong Sang , Suh Young-Ah , Jang Se Jin , Choi Eun Kyung , Lee Jung Shin , Jin Dong-Hoon , Kim Tae Won 
Published: September 2015

AbstractThe MET receptor tyrosine kinase, the receptor for hepatocyte growth factor (HGF), has been implicated in cancer growth, invasion, migration, angiogenesis, and metastasis in a broad variety of human cancers, including human hepatocellular carcinoma (HCC). Recently, MET was suggested to be a potential target for the personalized treatment of HCC with an active HGF–MET signaling pathway. However, the mechanisms of resistance to MET inhibitors need to be elucidated to provide effective treatment. Here, we show that HCC cells exhibit different sensitivities to the MET inhibitor PHA665752, depending on the phosphorylation status of FGFR. Treatment of cells expressing both phospho-FGFR and phospho-MET with the inhibitor PHA665752 did not cause growth inhibition and cell death, whereas treatment with AZD4547, a pan-FGFR inhibitor, resulted in decreased colony formation and cleavage of caspase-3. Moreover, silencing of endogenous FGFR1 and FGFR2 by RNAi of HCC cells expressing phospho-FGFR, phospho-FGFR2, and phospho-MET overcame the resistance to PHA665752 treatment. Treatment of primary cancer cells from patients with HCC expressing both phospho-FGFR and phospho-MET with PHA665752 did not induce cell death, whereas AZD4547 treatment induced cell death through the cleavage of caspase-3. In addition, treatment of cells resistant to PHA665752 with AZD4547 abrogated the activation of downstream effectors of cell growth, proliferation, and survival. On the basis of these results, we conclude that the FGFR pathway is critical for HCC survival, and that targeting this pathway with AZD4547 may be beneficial for the treatment of patients with HCC-expressing phospho-FGFR and phospho-MET. Mol Cancer Ther; 14(11); 2613–22. ©2015 AACR.
Sarcoma Cell Line Screen of Oncology Drugs and Investigational Agents Identifies Patterns Associated with Gene and microRNA Expression
Authors: Teicher Beverly A. , Polley Eric , Kunkel Mark , Evans David , Silvers Thomas , Delosh Rene , Laudeman Julie , Ogle Chad , Reinhart Russell , Selby Michael , Connelly John , Harris Erik , Monks Anne , Morris Joel 
Published: September 2015

AbstractThe diversity in sarcoma phenotype and genotype make treatment of this family of diseases exceptionally challenging. Sixty-three human adult and pediatric sarcoma lines were screened with 100 FDA-approved oncology agents and 345 investigational agents. The investigational agents' library enabled comparison of several compounds targeting the same molecular entity allowing comparison of target specificity and heterogeneity of cell line response. Gene expression was derived from exon array data and microRNA expression was derived from direct digital detection assays. The compounds were screened against each cell line at nine concentrations in triplicate with an exposure time of 96 hours using Alamar blue as the endpoint. Results are presented for inhibitors of the following targets: aurora kinase, IGF-1R, MEK, BET bromodomain, and PARP1. Chemical structures, IC50 heat maps, concentration response curves, gene expression, and miR expression heat maps are presented for selected examples. In addition, two cases of exceptional responders are presented. The drug and compound response, gene expression, and microRNA expression data are publicly available at http://sarcoma.cancer.gov. These data provide a unique resource to the cancer research community. Mol Cancer Ther; 14(11); 2452–62. ©2015 AACR.