bluuebunny/crossref_metadata_2025_split huggingface dataset:
Additional disulfide bonds in insulin: Prediction, recombinant expression, receptor binding affinity, and stability
Authors: Vinther Tine N. , Pettersson Ingrid , Huus Kasper , Schlein Morten , Steensgaard Dorte B. , Sørensen Anders , Jensen Knud J. , Kjeldsen Thomas , Hubalek František 
Published: January 2015

AbstractThe structure of insulin, a glucose homeostasis‐controlling hormone, is highly conserved in all vertebrates and stabilized by three disulfide bonds. Recently, we designed a novel insulin analogue containing afourth disulfide bond located between positions A10‐B4. The N‐terminus of insulin's B‐chain is flexible and can adapt multiple conformations. We examined how well disulfide bond predictions algorithms could identify disulfide bonds in this region of insulin. In order to identify stable insulin analogues with additional disulfide bonds, which could be expressed, the Cβcut‐off distance had to be increased in many instances and single X‐ray structures as well as structures from MD simulations had to be used. The analogues that were identified by the algorithm without extensive adjustments of the prediction parameters were more thermally stable as assessed by DSC and CD and expressed in higher yields in comparison to analogues with additional disulfide bonds that were more difficult to predict. In contrast, addition of thefourth disulfide bond rendered all analogues resistant to fibrillation under stress conditions and all stable analogues bound to the insulin receptor with picomolar affinities. Thus activity and fibrillation propensity did not correlate with the results from the prediction algorithm.Statement: A fourth disulfide bond has recently been introduced into insulin, a small two‐chain protein containing three native disulfide bonds. Here we show that a prediction algorithm predicts four additional four disulfide insulin analogues which could be expressed. Although the location of the additional disulfide bonds is only slightly shifted, this shift impacts both stability and activity of the resulting insulin analogues.
Energetic evaluation of binding modes in the C3d and Factor H (CCP 19‐20) complex
Authors: E. S. Harrison Reed , Gorham Ronald D. , Morikis Dimitrios 
Published: January 2015

AbstractAs a part of innate immunity, the complement system relies on activation of the alternative pathway (AP). While feed‐forward amplification generates an immune response towards foreign surfaces, the process requires regulation to prevent an immune response on the surface of host cells. Factor H (FH) is a complement protein secreted by native cells to negatively regulate the AP. In terms of structure, FH is composed of 20 complement‐control protein (CCP) modules that are structurally homologous but vary in composition and function. Mutations in these CCPs have been linked to states of autoimmunity. In particular, several mutations in CCP 19‐20 are correlated to atypical hemolytic uremic syndrome (aHUS). From crystallographic structures there are three putative binding sites of CCP 19‐20 on C3d. Since there has been some controversy over the primary mode of binding from experimental studies, we approach characterization of binding using computational methods. Specifically, we compare each binding mode in terms of electrostatic character, structural stability, dissociative and associative properties, and predicted free energy of binding. After a detailed investigation, we found two of the three binding sites to be similarly stable while varying in the number of contacts to C3d and in the energetic barrier to complex dissociation. These sites are likely physiologically relevant and may facilitate multivalent binding of FH CCP 19‐20 to C3b and either C3d or host glycosaminoglycans. We propose thermodynamically stable binding with modules 19 and 20, the latter driven by electrostatics, acting synergistically to increase the apparent affinity of FH for host surfaces.
Androgens regulate SMAD ubiquitination regulatory factor‐1 expression and prostate cancer cell invasion
Authors: Gang Xiaokun , Wang Guixia , Huang Haojie 
Published: January 2015

BACKGROUNDProstate cancer (PCa) is the most commonly diagnosed male cancer in the United States and is a hormone‐driven disease. Androgens have been recognized as a major promoter of PCa development and progression. However, the mechanism of androgen action in PCa, especially in PCa cell invasion and metastasis remains largely unclear. SMAD ubiquitination regulatory factor‐1 (SMURF1) is a C2‐WW‐HECT‐domain E3 ubiquitin ligase that plays important roles in cancer cell metastasis. Whether there is a relationship between androgens and SMURF1 expression is not known.METHODSThe effect of androgens on the expression of SMURF1 in PCa cell lines was examined by Western blot analyses and reverse transcription‐polymerase chain reaction (RT‐PCR). Gene transfection was performed by electroporation to manipulate the expression levels of proteins studied. The binding of AR to the SMURF1 gene enhancer was determined by chromatin immunoprecipitation (ChIP) assay. Cell migration and invasion was measured by wound healing and Matrigel invasion assays, respectively.RESULTSWe found that expression of SMURF1 is upregulated by androgens in PCa cell lines and that this effect of androgens is mediated through the androgen receptor (AR). We further showed that androgens regulate SMURF1 expression at transcriptional level and provided evidence that AR transcriptionally activates SMURF1 by binding to its enhancer that contains a canonical half androgen responsive element (ARE). Finally, we demonstrated that SMURF1 is important for androgen‐induced invasion of PCa cells.CONCLUSIONSWe demonstrate for the first time that SMURF1 is a bona fide target gene of the AR. Our findings also suggest a potential role of SMURF1 in PCa metastasis. Prostate 75: 561–572, 2015. © 2015 Wiley Periodicals, Inc.
The complexity and structural diversity of ant venom peptidomes is revealed by mass spectrometry profiling
Authors: Touchard Axel , Koh Jennifer M. S. , Aili Samira R. , Dejean Alain , Nicholson Graham M. , Orivel Jérôme , Escoubas Pierre 
Published: January 2015

RationaleCompared with other animal venoms, ant venoms remain little explored. Ants have evolved complex venoms to rapidly immobilize arthropod prey and to protect their colonies from predators and pathogens. Many ants have retained peptide‐rich venoms that are similar to those of other arthropod groups.MethodsWith the goal of conducting a broad and comprehensive survey of ant venom peptide diversity, we investigated the peptide composition of venoms from 82 stinging ant species from nine subfamilies using matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (MALDI‐TOFMS). We also conducted an in‐depth investigation of eight venoms using reversed‐phase high‐performance liquid chromatography (RP‐HPLC) separation coupled with offline MALDI‐TOFMS.ResultsOur results reveal that the peptide compositions of ant venom peptidomes from both poneroid and formicoid ant clades comprise hundreds of small peptides (<4 kDa), while large peptides (>4 kDa) are also present in the venom of formicoids. Chemical reduction revealed the presence of disulfide‐linked peptides in most ant subfamilies, including peptides structured by one, two or three disulfide bonds as well as dimeric peptides reticulated by three disulfide bonds.ConclusionsThe biochemical complexity of ant venoms, associated with an enormous ecological and taxonomic diversity, suggests that stinging ant venoms constitute a promising source of bioactive molecules that could be exploited in the search for novel drug and biopesticide leads. Copyright © 2015 John Wiley & Sons, Ltd.
Schlieren visualization of fluid dynamics effects in direct analysis in real time mass spectrometry
Authors: Curtis Matthew , Keelor Joel D. , Jones Christina M. , Pittman Jennifer J. , Jones Patrick R. , Sparkman O. David , Fernández Facundo M. 
Published: January 2015

RationaleThe success of ambient analysis using plasma‐based ion sources depends heavily on fluid dynamics and mass transport efficiency in the sample region. To help characterize the influence of these determining factors, visualization of the gas flow profile for a Direct Analysis in Real Time (DART) ion source at the mass spectrometer atmospheric pressure (AP) interface was performed using the Schlieren technique.MethodsThe DART helium flow pattern was imaged in model systems incorporating different interface designs, i.e. skimmer or capillary inlet, and for sampling strategies using several types of traditional DART sample probes including a glass capillary, swab, and drug tablet. Notably, Schlieren experiments were conducted on instruments equipped with the gas‐ion separator tube (GIST) adapter and Vapur® pump, and on setups featuring the transmission mode (TM) DART module used in standard practice.ResultsDART sources were seen to expel a collimated, highly laminar helium stream across interface distances up to ~8 cm. The helium stream was robust to the influence of gas temperature (50–500 °C) and flow rate (≤3.5 L min–1), but considerable DART gas deflection or full disruption was observed in each sampling scenario. The severity of the flow disturbance depended on probe size and placement, the GIST/Vapur® settings, or counter‐current gas movements present at the interface.ConclusionsThe real‐time Schlieren visualizations introduced in this work provide new insight on the fluid dynamics within the DART‐MS sample gap while also helping to identify those experimental parameters requiring optimization for improved transmission. Copyright © 2015 John Wiley & Sons, Ltd.
Analysis of neonicotinoids from plant material by desorption atmospheric pressure photoionization‐mass spectrometry
Authors: Vaikkinen Anu , Schmidt Henning S. , Kiiski Iiro , Rämö Sari , Hakala Kati , Haapala Markus , Kostiainen Risto , Kauppila Tiina J. 
Published: January 2015

RationaleNeonicotinoids are widely used insecticides which have been shown to affect the memory and learning abilities of honey bees, and are suspected to play a part in the unexplainable, large‐scale loss of honey bee colonies. Fast methods, such as ambient mass spectrometry (MS), for their analysis from a variety of matrices are necessary to control the use of forbidden products and study the spreading of insecticides in nature.MethodsThe feasibilities of two ambient MS methods, desorption electrospray ionization (DESI) and desorption atmospheric pressure photoionization (DAPPI), for the analysis of five most used neonicotinoid compounds, thiacloprid, acetamiprid, clothianidin, imidacloprid and thiamethoxam, were tested. In addition, DAPPI was used to analyze fresh rose leaves treated with commercially available thiacloprid insecticide and dried and powdered turnip rape flowers, which had been collected from a field treated with thiacloprid‐containing insecticide.ResultsDAPPI was found to be more sensitive than DESI, with 2–11 times better signal‐to‐noise ratios, and limits of detection at 0.4–5.0 fmol for the standard compounds. DAPPI was able to detect thiacloprid from the rose leaves even 2.5 months after the treatment and from the turnip rape flower samples collected from a field. The analysis of plant material by DAPPI did not require extraction or other sample preparation.ConclusionsDAPPI was found to be suitable for the fast and direct qualitative analysis of thiacloprid neonicotinoid from plant samples. It shows promise as a fast tool for screening of forbidden insecticides, or studying the distribution of insecticides in nature. Copyright © 2015 John Wiley & Sons, Ltd.
SAKE: scalable authenticated key exchange for mobile e‐health networks
Authors: Liu Weiran , Liu Jianwei , Wu Qianhong , Susilo Willy , Deng Hua , Qin Bo 
Published: January 2015

AbstractMobile e‐Health Network (MHN) is an emerging cloud‐aided networking application across the entire range of functions involved in e‐Health systems. It is important to establish secure channels between users because the data transmitted in MHNs are private, for example, personal electronic healthcare records. It is of great significance to employ key management mechanism and encrypt the data before transmitting in MHNs. However, secure key management is challenging in MHNs because of its highly dynamic and large‐scale nature. In this paper, we first model MHNs and formalize a hierarchical network architecture mirroring the administrative hierarchy and dynamic autonomy in MHNs in the real world. We next present a virtual MHN architecture with only three levels yet suitable to realistic MHNs with arbitrary hierarchical levels. By exploiting the virtual architecture, we propose an efficient authenticated key exchange framework to secure MHNs. We realize a scalable authenticated key exchange scheme with a dedicated variant of a recent hierarchical identity‐based signature and the well‐known Diffie–Hellman key exchange protocol. Theoretical analyses and experimental results show that scalable authenticated key exchange is secure and scalable and hence is practical to secure MHNs. Copyright © 2015 John Wiley & Sons, Ltd.
Dissecting the roles of TRBP and PACT in double‐stranded RNA recognition and processing of noncoding RNAs
Authors: Heyam Alex , Lagos Dimitris , Plevin Michael 
Published: January 2015

HIV TAR RNA‐binding protein (TRBP) and Protein Activator of PKR (PACT) are double‐stranded (ds) RNA‐binding proteins that participate in both small regulatory RNA biogenesis and the response to viral dsRNA. Despite considerable progress toward understanding the structure–function relationship of TRBP and PACT, their specific roles in these seemingly distinct cellular pathways remain unclear. Both proteins are composed of three copies of the double‐stranded RNA‐binding domain, two of which interact with dsRNA, while the C‐terminal copy mediates protein–protein interactions. PACT and TRBP are found in a complex with the endonuclease Dicer and facilitate processing of immature microRNAs. Their precise contribution to the Dicing step has not yet been defined: possibilities include precursor recruitment, rearrangement of dsRNA within the complex, loading the processed microRNA into the RNA‐induced silencing complex, and distinguishing different classes of small dsRNA. TRBP and PACT also interact with the viral dsRNA sensors retinoic acid‐inducible gene I (RIG‐I) and double‐stranded RNA‐activated protein kinase (PKR). Current models suggest that PACT enables RIG‐I to detect a wider range of viral dsRNAs, while TRBP and PACT exert opposing regulatory effects on PKR. Here, the evidence that implicates TRBP and PACT in regulatory RNA processing and viral dsRNA sensing is reviewed and discussed in the context of their molecular structure. The broader implications of a link between microRNA biogenesis and the innate antiviral response pathway are also considered. WIREs RNA 2015, 6:271–289. doi: 10.1002/wrna.1272This article is categorized under:

RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms
Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs
Functional roles of alternative splicing factors in human disease
Authors: Cieply Benjamin , Carstens Russ P. 
Published: January 2015

Alternative splicing (AS) is an important mechanism used to generate greater transcriptomic and proteomic diversity from a finite genome. Nearly all human gene transcripts are alternatively spliced and can produce protein isoforms with divergent and even antagonistic properties that impact cell functions. Many AS events are tightly regulated in a cell‐type or tissue‐specific manner, and at different developmental stages. AS is regulated by RNA‐binding proteins, including cell‐ or tissue‐specific splicing factors. In the past few years, technological advances have defined genome‐wide programs of AS regulated by increasing numbers of splicing factors. These splicing regulatory networks (SRNs) consist of transcripts that encode proteins that function in coordinated and related processes that impact the development and phenotypes of different cell types. As such, it is increasingly recognized that disruption of normal programs of splicing regulated by different splicing factors can lead to human diseases. We will summarize examples of diseases in which altered expression or function of splicing regulatory proteins has been implicated in human disease pathophysiology. As the role of AS continues to be unveiled in human disease and disease risk, it is hoped that further investigations into the functions of numerous splicing factors and their regulated targets will enable the development of novel therapies that are directed at specific AS events as well as the biological pathways they impact. WIREs RNA 2015, 6:311–326. doi: 10.1002/wrna.1276This article is categorized under:

RNA Processing > Splicing Mechanisms
RNA Processing > Splicing Regulation/Alternative Splicing
RNA in Disease and Development > RNA in Disease
Preparation of Aluminum Hydrides with Chelating Anilido‐Imine Ligands by Addition of an Al–H Bond to a C=N Bond
Authors: Wang Weiwei , Yang Zhi , Ma Xiaoli , Roesky Herbert W. , Ju Yingxin , Hao Pengfei 
Published: January 2015

AbstractReacting o‐C6H4F(CH = NC6H3iPr2‐2,6) (L) with H3Al·NMe3 resulted in the aluminum dihydride with coordinated NMe3 of composition [o‐C6H4F(CH2NC6H3iPr2‐2,6)]AlH2(NMe3)(1). Furthermore, the aluminum monohydride [o‐C6H4N(C6H3iPr2‐2,6)(CH2NC6H3iPr2‐2,6)]AlH(NMe3) (2) was prepared by treatment of the anilido‐imine ligand o‐C6H4N(C6H3iPr2‐2,6)(CH = NC6H3iPr2‐2,6) (L*) with H3Al·NMe3 in high yield. The formations of the two complexes both involve aluminum hydride addition to the C=N double bond. Compounds 1 and 2 were characterized by 1H NMR and IR spectroscopic, elementary analysis, and single‐crystal X‐ray diffraction studies.
Oxidative Addition of Diethylchalcogenanes to Lappert's Germylene and Stannylene
Authors: Bendt Georg , Lapsien Silvia , Steiniger Phillip , Bläser Dieter , Wölper Christoph , Schulz Stephan 
Published: January 2015

AbstractOxidative addition of diethyldichalcogenanes Et2E2 (E = S, Se, Te) to bis[bis(trimethylsilyl]amido]germylene and ‐stannylene M[N(SiMe3)2]2 (M = Ge, Sn) proceed with formation of the corresponding bis(ethylchalcogenato)germanes (Me3Si)2N)2Ge(EEt)2 [E = S (1), Se (2), Te (3)] and ‐stannanes (Me3Si)2N)2Sn(EEt)2 [E = S (4), Se (5), Te (6)]. The solid state structures of 1–6 were determined by single‐crystal X‐ray diffraction.
Risk Factors for Conversion of Laparoscopic Colorectal Surgery to Open Surgery: Does Conversion Worsen Outcome?
Authors: Masoomi Hossein , Moghadamyeghaneh Zhobin , Mills Steven , Carmichael Joseph C. , Pigazzi Alessio , Stamos Michael J. 
Published: January 2015

AbstractIntroductionThe utilization of laparoscopy in colorectal surgery is increasing. However, conversion to open surgery remains relatively high.ObjectiveWe evaluated (1) conversion rates in laparoscopic colorectal surgery; (2) the outcomes of converted cases compared with successful laparoscopic and open colorectal operations; (3) predictive risk factors of conversion of laparoscopic colorectal surgery to open surgery.MethodsUsing the National Inpatient Sample database, we examined the clinical data of patients who underwent colon and rectal resection from 2009 to 2010. Multivariate regression analysis was performed to identify factors predictive for conversion of laparoscopic to open operation.ResultsA total of 207,311 patients underwent intended laparoscopic colorectal resection during this period. The conversion rate was 16.6 %. Considering resection type and pathology, the highest conversion rates were observed in proctectomy (31.4 %) and Crohn’s disease (20.2 %). Using multivariate regression analysis, Crohn’s disease (adjusted odds ratio [AOR], 2.80), prior abdominal surgery (AOR, 2.45), proctectomy (AOR, 2.42), malignant pathology (AOR, 1.90), emergent surgery (AOR, 1.82), obesity (AOR, 1.63), and ulcerative colitis (AOR, 1.60) significantly impacted the risk of conversion. Compared with patients who were successfully completed laparoscopically, converted patients had a significantly higher complication rate (laparoscopic: 23 %; vs. converted: 35.2 % vs. open: 35.3 %), a higher in‐hospital mortality rate (laparoscopic: 0.5 %; vs. converted: 0.6 %; vs. open: 1.7 %) and a longer mean hospital stay (laparoscopic: 5.4 days; vs. converted: 8.1 days; vs. open: 8.4 days); however, converted patients had better outcomes compared with the open group.ConclusionsThe conversion rate in colorectal surgery was 16.6 %. Converted patients had significantly higher rates of morbidity and mortality compared to successfully completed laparoscopic cases, although lower than open cases. Crohn’s disease, prior abdominal surgery, and proctectomy are the strongest predictors for conversion of laparoscopic to open in colorectal operations.
Hyperplastic polyposis: a case report
Authors: Flauzino Thiago Almeida , Fardin Gabriela N.S. , Sena Adriana F. , Gama Leonardo R.F. , Ribeiro Flávia L.M. , Loureiro Giovanni J.Z. , Gama Luciano P.N. , Gama Rossini C. 
Published: January 2015

Abstract
Objective The authors present a case report of hyperplastic polyposis syndrome from the Coloproctology Service, Vitória Apart Hospital, Vitória-ES.
Case study Our case is a 24-year-old man who suffered from fatigue, malaise and microcytic and hypochromic anemia, whose upper digestive endoscopy presented several hyperplastic polyps in the stomach and whose colonoscopy revealed colonic polyposis mainly in the right colon; the histopathology showed tubular adenoma with moderate atypia in the ascending colon. Thus, a videolaparoscopic right colectomy was performed; the analysis of the surgical fragment showed multiple (more than 30) polyps distributed through the cecum and ascending colon.
Conclusion The histopathological diagnosis of hyperplastic polyposis is a challenging task. In general, most polyps are hyperplastic, but serrated and classic adenomas also occur. These associated adenomatous injuries can be the cause of malignant transformation. So far, there is no consensus about the appropriate treatment; however, a colectomy procedure may be beneficial in a scenario of a large number of hyperplastic polyps, concurrent serrated adenomas, or multiple high-risk adenomatous lesions.