bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative omics connects N-glycoproteome-wide alterations with pathways and regulatory events in induced pluripotent stem cells
Authors: Sudhir Putty-Reddy , Kumari Madireddy Pavana , Hsu Wei-Ting , Chen Chein-Hung , Kuo Hung-Chih , Chen Chung-Hsuan 
Published: November 2016

AbstractMolecular-level differences ranging from genomes to proteomes, but not N-glycoproteomes, between human induced pluripotent stem cells (hiPSCs) and embryonic stem cells (hESCs) have been assessed to gain insights into cell reprogramming and induced pluripotency. Our multiplexed quantitative N-glycoproteomics study identified altered N-glycoproteins that significantly regulate cell adhesion processes in hiPSCs compared to hESCs. The integrative proteomics and functional network analyses of the altered N-glycoproteins revealed their significant interactions with known PluriNet (pluripotency-associated network) proteins. We found that these interactions potentially regulate various signaling pathways including focal adhesion, PI3K-Akt signaling, regulation of actin cytoskeleton, and spliceosome. Furthermore, the integrative transcriptomics analysis revealed that imperfectly reprogrammed subunits of the oligosaccharyltransferase (OST) and dolichol-phosphate-mannose synthase (DPM) complexes were potential candidate regulatory events for the altered N-glycoprotein levels. Together, the results of our study suggest that imperfect reprogramming of the protein complexes linked with the N-glycosylation process may result in N-glycoprotein alterations that affect induced pluripotency through their functional protein interactions.
The influence of warm ischemia elimination on kidney injury during transplantation – clinical and molecular study
Authors: Kamińska Dorota , Kościelska-Kasprzak Katarzyna , Chudoba Paweł , Hałoń Agnieszka , Mazanowska Oktawia , Gomółkiewicz Agnieszka , Dzięgiel Piotr , Drulis-Fajdasz Dominika , Myszka Marta , Lepiesza Agnieszka , Polak Wojciech , Boratyńska Maria , Klinger Marian 
Published: November 2016

AbstractKidney surface cooling was used during implantation to assess the effect of warm ischemia elimination on allograft function, histological changes and immune-related gene expression. 23 recipients were randomly assigned to a group operated on with kidney surface cooling during implantation (ice bag technique, IBT group), and the other 23 recipients receiving the contralateral kidney from the same donor were operated on with a standard technique. Three consecutive kidney core biopsies were obtained during the transplantation procedure: after organ recovery, after cold ischemia and after reperfusion. Gene expression levels were determined using low-density arrays (Format 32, TaqMan). The IBT group showed a significantly lower rate of detrimental events (delayed graft function and/or acute rejection, p = 0.015) as well as higher glomerular filtration rate on day 14 (p = 0.026). A greater decrease of MMP9 and LCN2 gene expression was seen in the IBT group during total ischemia (p = 0.003 and p = 0.018). Elimination of second warm ischemia reduced the number of detrimental events after kidney transplantation, and thus had influence on the short-term but not long-term allograft function. Surface cooling of the kidney during vascular anastomosis may reduce some detrimental effects of immune activation resulting from both brain death and ischemia-reperfusion injury.
Inhibition of hydrogen sulfide biosynthesis sensitizes lung adenocarcinoma to chemotherapeutic drugs by inhibiting mitochondrial DNA repair and suppressing cellular bioenergetics
Authors: Szczesny Bartosz , Marcatti Michela , Zatarain John R. , Druzhyna Nadiya , Wiktorowicz John E. , Nagy Péter , Hellmich Mark R. , Szabo Csaba 
Published: November 2016

AbstractTherapeutic manipulation of the gasotransmitter hydrogen sulfide (H2S) has recently been proposed as a novel targeted anticancer approach. Here we show that human lung adenocarcinoma tissue expresses high levels of hydrogen sulfide (H2S) producing enzymes, namely, cystathionine beta-synthase (CBS), cystathionine gamma lyase (CSE) and 3-mercaptopyruvate sulfurtransferase (3-MST), in comparison to adjacent lung tissue. In cultured lung adenocarcinoma but not in normal lung epithelial cells elevated H2S stimulates mitochondrial DNA repair through sulfhydration of EXOG, which, in turn, promotes mitochondrial DNA repair complex assembly, thereby enhancing mitochondrial DNA repair capacity. In addition, inhibition of H2S-producing enzymes suppresses critical bioenergetics parameters in lung adenocarcinoma cells. Together, inhibition of H2S-producing enzymes sensitize lung adenocarcinoma cells to chemotherapeutic agents via induction of mitochondrial dysfunction as shown in in vitro and in vivo models, suggesting a novel mechanism to overcome tumor chemoresistance.
Changeover from signalling to energy-provisioning lipids during transition from colostrum to mature milk in the giant panda (Ailuropoda melanoleuca)
Authors: Zhang Tong , Watson David G. , Zhang Rong , Hou Rong , Loeffler I. Kati , Kennedy Malcolm W. 
Published: November 2016

AbstractAmong the large placental mammals, ursids give birth to the most altricial neonates with the lowest neonatal:maternal body mass ratios. This is particularly exemplified by giant pandas. To examine whether there is compensation for the provision of developmentally important nutrients that other species groups may provide in utero, we examined changes in the lipids of colostrum and milk with time after birth in giant pandas. Lipids that are developmental signals or signal precursors, and those that are fundamental to nervous system construction, such as docosahexaenoic acid (DHA) and phosphatidylserines, appear early and then fall dramatically in concentration to a baseline at 20–30 days. The dynamics of lysophosphatidic acid and eicosanoids display similar patterns, but with progressive differences between mothers. Triglycerides occur at relatively low levels initially and increase in concentration until a plateau is reached at about 30 days. These patterns indicate an early provision of signalling lipids and their precursors, particularly lipids crucial to brain, retinal and central nervous system development, followed by a changeover to lipids for energy metabolism. Thus, in giant pandas, and possibly in all bears, lactation is adapted to provisioning a highly altricial neonate to a degree that suggests equivalence to an extension of gestation.
Using genome-wide CRISPR library screening with library resistant DCK to find new sources of Ara-C drug resistance in AML
Authors: Kurata Morito , Rathe Susan K. , Bailey Natashay J. , Aumann Natalie K. , Jones Justine M. , Veldhuijzen G. Willemijn , Moriarity Branden S. , Largaespada David A. 
Published: November 2016

AbstractAcute myeloid leukemia (AML) can display de novo or acquired resistance to cytosine arabinoside (Ara-C), a primary component of induction chemotherapy. To identify genes capable of independently imposing Ara-C resistance, we applied a genome-wide CRISPR library to human U937 cells and exposed to them to Ara-C. Interestingly, all drug resistant clones contained guide RNAs for DCK. To avoid DCK gene modification, gRNA resistant DCK cDNA was created by the introduction of silent mutations. The CRISPR screening was repeated using the gRNA resistant DCK, and loss of SLC29A was identified as also being capable of conveying Ara-C drug resistance. To determine if loss of Dck results in increased sensitivity to other drugs, we conducted a screen of 446 FDA approved drugs using two Dck-defective BXH-2 derived murine AML cell lines and their Ara-C sensitive parental lines. Both cell lines showed an increase in sensitivity to prednisolone. Guide RNA resistant cDNA rescue was a legitimate strategy and multiple DCK or SLC29A deficient human cell clones were established with one clone becoming prednisolone sensitive. Dck-defective leukemic cells may become prednisolone sensitive indicating prednisolone may be an effective adjuvant therapy in some cases of DCK-negative AML.
Identification of a two-component Class IIb bacteriocin in Streptococcus pyogenes by recombinase-based in vivo expression technology
Authors: Armstrong Brent D. , Herfst Christine A. , Tonial Nicholas C. , Wakabayashi Adrienne T. , Zeppa Joseph J. , McCormick John K. 
Published: November 2016

AbstractStreptococcus pyogenes is a globally prominent bacterial pathogen that exhibits strict tropism for the human host, yet bacterial factors responsible for the ability of S. pyogenes to compete within this limited biological niche are not well understood. Using an engineered recombinase-based in vivo expression technology (RIVET) system, we identified an in vivo-induced promoter region upstream of a predicted Class IIb bacteriocin system in the M18 serotype S. pyogenes strain MGAS8232. This promoter element was not active under in vitro laboratory conditions, but was highly induced within the mouse nasopharynx. Recombinant expression of the predicted mature S. pyogenes bacteriocin peptides (designated SpbM and SpbN) revealed that both peptides were required for antimicrobial activity. Using a gain of function experiment in Lactococcus lactis, we further demonstrated S. pyogenes immunity function is encoded downstream of spbN. These data highlight the importance of bacterial gene regulation within appropriate environments to help understand mechanisms of niche adaptation by bacterial pathogens.
Limited mitogenomic degradation in response to a parasitic lifestyle in Orobanchaceae
Authors: Fan Weishu , Zhu Andan , Kozaczek Melisa , Shah Neethu , Pabón-Mora Natalia , González Favio , Mower Jeffrey P. 
Published: November 2016

AbstractIn parasitic plants, the reduction in plastid genome (plastome) size and content is driven predominantly by the loss of photosynthetic genes. The first completed mitochondrial genomes (mitogenomes) from parasitic mistletoes also exhibit significant degradation, but the generality of this observation for other parasitic plants is unclear. We sequenced the complete mitogenome and plastome of the hemiparasite Castilleja paramensis (Orobanchaceae) and compared them with additional holoparasitic, hemiparasitic and nonparasitic species from Orobanchaceae. Comparative mitogenomic analysis revealed minimal gene loss among the seven Orobanchaceae species, indicating the retention of typical mitochondrial function among Orobanchaceae species. Phylogenetic analysis demonstrated that the mobile cox1 intron was acquired vertically from a nonparasitic ancestor, arguing against a role for Orobanchaceae parasites in the horizontal acquisition or distribution of this intron. The C. paramensis plastome has retained nearly all genes except for the recent pseudogenization of four subunits of the NAD(P)H dehydrogenase complex, indicating a very early stage of plastome degradation. These results lend support to the notion that loss of ndh gene function is the first step of plastome degradation in the transition to a parasitic lifestyle.
Effects of sedimentation on soil physical and chemical properties and vegetation characteristics in sand dunes at the Southern Dongting Lake region, China
Authors: Pan Ying , Zhang Hao , Li Xu , Xie Yonghong 
Published: November 2016

AbstractSedimentation is recognized as a major factor determining the ecosystem processes of lake beaches; however, the underlying mechanisms, especially in freshwater sand dunes, have been insufficiently studied. To this end, nine belt transects from nine freshwater sand dunes, classified into low (<23.7 m), medium (25.4–26.0 m), and high-elevation groups (>28.1 m) based on their elevations in 1972, were sampled to investigate differences in sedimentation rate and soil and vegetation characteristics in Southern Dongting Lake, China. Sedimentation rate, soil sand content, and soil pH increased, whereas soil clay, fine silt, moisture (MC), organic matter (OM), total N, and total K content, in addition to the growth and biodiversity of sand dune plants generally decreased with decreasing belt transect elevation. Regression analyses revealed that the negative effects of sedimentation on the ecosystem functions of sand dunes could be attributed to higher fine sand content in deposited sediments and stronger inhibition of plant growth. These results are consistent with previous studies performed in coastal sand dunes, which highlights the importance of sedimentation in determining ecological processes.
Constructing safe and durable antibacterial textile surfaces using a robust graft-to strategy via covalent bond formation
Authors: He Liang , Li Sha , Chung Cordelia T. W. , Gao Chang , Xin John H. 
Published: November 2016

AbstractRecently zwitterionic materials have been widely applied in the biomedical and bioengineering fields due to their excellent biocompatibility. Inspired by these, this study presents a graft-to strategy via covalent bond formation to fabricate safe and durable antibacterial textile surfaces. A novel zwitterionic sulfobetaine containing triazine reactive group was specifically designed and synthesized. MTT assay showed that it had no obvious cytotoxicity to human skin HaCaT cells as verified by ca. 89.9% relative viability at a rather high concentration of 0.8 mg·mL−1. In the evaluation for its skin sensitization, the maximum score for symptoms of erythema and edema in all tests were 0 in all observation periods. The sulfobetaine had a hydrophilic nature and the hydrophilicity of the textiles was enhanced by 43.9% when it was covalently grafted onto the textiles. Moreover, the textiles grafted with the reactive sulfobetaine exhibited durable antibacterial activities, which was verified by the fact that they showed antibacterial rates of 97.4% against gram-positive S. aureus and 93.2% against gram-negative E. coli even after they were laundered for 30 times. Therefore, the titled zwitterionic sulfobetaine is safe to human for healthcare and wound dressing and shows a promising prospect on antibacterial textile application.
Sensitivity of El Niño intensity and timing to preceding subsurface heat magnitude
Authors: Ballester Joan , Petrova Desislava , Bordoni Simona , Ben Cash  , García-Díez Markel , Rodó Xavier 
Published: November 2016

AbstractDespite extensive ongoing efforts on improving the long-term prediction of El Niño-Southern Oscillation, the predictability in state-of-the-art operational schemes remains limited by factors such as the spring barrier and the influence of atmospheric winds. Recent research suggests that the 2014/15 El Niño (EN) event was stalled as a result of an unusually strong basin-wide easterly wind burst in June, which led to the discharge of a large fraction of the subsurface ocean heat. Here we use observational records and numerical experiments to explore the sensitivity of EN to the magnitude of the heat buildup occurring in the ocean subsurface 21 months in advance. Our simulations suggest that a large increase in heat content during this phase can lead to basin-wide uniform warm conditions in the equatorial Pacific the winter before the occurrence of a very strong EN event. In our model configuration, the system compensates any initial decrease in heat content and naturally evolves towards a new recharge, resulting in a delay of up to one year in the occurrence of an EN event. Both scenarios substantiate the non-linear dependency between the intensity of the subsurface heat buildup and the magnitude and timing of subsequent EN episodes.
Structural basis of the high thermal stability of the histone-like HU protein from the mollicute Spiroplasma melliferum KC3
Authors: Boyko Konstantin M. , Rakitina Tatiana V. , Korzhenevskiy Dmitry A. , Vlaskina Anna V. , Agapova Yuliya K. , Kamashev Dmitry E. , Kleymenov Sergey Y. , Popov Vladimir O. 
Published: November 2016

AbstractThe three-dimensional structure of the histone-like HU protein from the mycoplasma Spiroplasma melliferum KC3 (HUSpm) was determined at 1.4 Å resolution, and the thermal stability of the protein was evaluated by differential scanning calorimetry. A detailed analysis revealed that the three-dimensional structure of the HUSpm dimer is similar to that of its bacterial homologues but is characterized by stronger hydrophobic interactions at the dimer interface. This HUSpm dimer interface lacks salt bridges but is stabilized by a larger number of hydrogen bonds. According to the DSC data, HUSpm has a high denaturation temperature, comparable to that of HU proteins from thermophilic bacteria. To elucidate the structural basis of HUSpm thermal stability, we identified amino acid residues potentially responsible for this property and modified them by site-directed mutagenesis. A comparative analysis of the melting curves of mutant and wild-type HUSpm revealed the motifs that play a key role in protein thermal stability: non-conserved phenylalanine residues in the hydrophobic core, an additional hydrophobic loop at the N-terminal region of the protein, the absence of the internal cavity present at the dimer interface of some HU proteins, and the presence of additional hydrogen bonds between the monomers that are missing in homologous proteins.
Epac1 interacts with importin β1 and controls neurite outgrowth independently of cAMP and Rap1
Authors: Baameur Faiza , Singhmar Pooja , Zhou Yong , Hancock John F. , Cheng Xiaodong , Heijnen Cobi J. , Kavelaars Annemieke 
Published: November 2016

AbstractExchange protein directly activated by cAMP-1 (Epac1) is a cAMP sensor that regulates multiple cellular functions including cellular migration, proliferation and differentiation. Classically, Epac1 is thought to exert its effects through binding of cAMP leading to a conformational change in Epac1 and its accumulation at the plasma membrane (PM) where it activates Rap1. In search for regulators of Epac1 activity, we show here that importin β1 (impβ1) is an Epac1 binding partner that prevents PM accumulation of Epac1. We demonstrate that in the absence of impβ1, endogenous as well as overexpressed Epac1 accumulate at the PM. Moreover, agonist-induced PM translocation of Epac1 leads to dissociation of Epac1 from impβ1. Localization of Epac1 at the PM in the absence of impβ1, requires residue R82 in its DEP domain. Notably, the PM accumulation of Epac1 in the absence of impβ1 does not require binding of cAMP to Epac1 and does not result in Rap1 activation. Functionally, PM accumulation of Epac1, an Epac1 mutant deficient in cAMP binding, or an Epac1 mutant tethered to the PM, is sufficient to inhibit neurite outgrowth. In conclusion, we uncover a cAMP-independent function of Epac1 at the PM and demonstrate that impβ1 controls subcellular localization of Epac1.
Exposure to extremely low frequency electromagnetic fields alters the behaviour, physiology and stress protein levels of desert locusts
Authors: Wyszkowska Joanna , Shepherd Sebastian , Sharkh Suleiman , Jackson Christopher W. , Newland Philip L. 
Published: November 2016

AbstractElectromagnetic fields (EMFs) are present throughout the modern world and are derived from many man-made sources including overhead transmission lines. The risks of extremely-low frequency (ELF) electromagnetic fields are particularly poorly understood especially at high field strengths as they are rarely encountered at ground level. Flying insects, however, can approach close to high field strength transmission lines prompting the question as to how these high levels of exposure affect behaviour and physiology. Here we utilise the accessible nervous system of the locust to ask how exposure to high levels of ELF EMF impact at multiple levels. We show that exposure to ELF EMFs above 4 mT leads to reduced walking. Moreover, intracellular recordings from an identified motor neuron, the fast extensor tibiae motor neuron, show increased spike latency and a broadening of its spike in exposed animals. In addition, hind leg kick force, produced by stimulating the extensor tibiae muscle, was reduced following exposure, while stress-protein levels (Hsp70) increased. Together these results suggest that ELF EMF exposure has the capacity to cause dramatic effects from behaviour to physiology and protein expression, and this study lays the foundation to explore the ecological significance of these effects in other flying insects.
Gesundheit und medizinscher und psychosozialer Versorgungsbedarf von akuten oder ehemaligen Drogenabhängigen im Alter (40+) – Eine Querschnittstudie
Authors: Wehrwein A. , Schröder G. , Lindert J. 
Published: November 2016

Zusammenfassung
Hintergrund: Ziel dieser Studie war es, Gesundheit, gesundheitsbezogene Lebensqualität und den Wohn-, Hilfe- und Pflegebedarf älterer (ehemals) Drogenabhängiger zu erfassen sowie zu untersuchen, ob der Gesundheitszustand mit dem Wohn-, Unterstützungs- und Pflegebedarf assoziiert ist.
Methode: Zunächst wurde die Grundgesamtheit mittels capture-recapture Verfahren erhoben. Im zweiten Schritt wurde eine Einrichtungen-basierte Querschnittserhebung in Stuttgart (2014) durchgeführt. Erfasst wurden soziodemografische Daten, gesundheitsbezogene Lebensqualität (SF-36) sowie Erkrankungen, derzeitiger Wohn-, Unterstützungs- und Pflegebedarf (Fragebogen 50plushiv), und Substanzkonsum („European Addiction Severity Index“). Die Daten wurden uni-, bi- und multivariat analysiert.
Ergebnisse: N=37 Personen (30% Frauen) nahmen an der Studie teil (Responserate: 10,5%). 89% leiden an mindestens einer Erkrankung. Werte der allgemeinen Gesundheit (p=0,011), der Vitalität (p<0,001), der sozialen Funktionsfähigkeit (p<0,001), des psychischen Wohlbefindens (p<0,001) sowie der körperlichen Summenskala (p=0,007) und der psychischen Summenskala (p<0,001) liegen signifikant unter den Werten der altersspezifischen Normpopulation (51–60 Jahre). 54% haben derzeit einen Unterstützungsbedarf. Selbstständigkeit sowie fortgesetzter Substanzkonsum im Alter ist den Teilnehmerinnen am wichtigsten.
Schlussfolgerung: Gesundheitsbezogene Lebensqualität und insbesondere soziale Funktionsfähigkeit scheint bei älteren (ehemals) Drogenabhängigen reduziert zu sein. Dies zeigt die Notwendigkeit spezifische Versorgungskonzepte für ältere Drogenabhängige entsprechend dieser Ergebnisse zu gestalten. Zur Replizierung der Ergebnisse wäre eine repräsentative Langzeitstudie zur Erfassung des medizinischen und psychosozialen Versorgungsbedarfes älterer Drogenabhängiger notwendig.
Methanobactin transport machinery
Authors: Dassama Laura M. K. , Kenney Grace E. , Ro Soo Y. , Zielazinski Eliza L. , Rosenzweig Amy C. 
Published: November 2016

SignificanceCopper is central to the metabolism of methanotrophs, methane-oxidizing bacteria that are of interest because of their potential applications in bioremediation and bioconversion processes. Methanotrophs convert methane to methanol using particulate methane monooxygenase (pMMO), a copper-dependent, membrane-bound enzyme. To fulfill pMMO’s high requirement for copper, methanotrophs secrete and re-internalize methanobactin, a peptide-derived, copper-chelating natural product (CuMbn). Here we characterize the protein machinery used for import and periplasmic transport of CuMbn. These data provide important insights into the molecular mechanisms of CuMbn recognition and handling.