bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ribosome biogenesis in replicating cells: Integration of experiment and theory
Authors: Earnest Tyler M. , Cole John A. , Peterson Joseph R. , Hallock Michael J. , Kuhlman Thomas E. , Luthey‐Schulten Zaida 
Published: June 2016

ABSTRACTRibosomes—the primary macromolecular machines responsible for translating the genetic code into proteins—are complexes of precisely folded RNA and proteins. The ways in which their production and assembly are managed by the living cell is of deep biological importance. Here we extend a recent spatially resolved whole‐cell model of ribosome biogenesis in a fixed volume [Earnest et al., Biophys J 2015, 109, 1117–1135] to include the effects of growth, DNA replication, and cell division. All biological processes are described in terms of reaction‐diffusion master equations and solved stochastically using the Lattice Microbes simulation software. In order to determine the replication parameters, we construct and analyze a series of Escherichia coli strains with fluorescently labeled genes distributed evenly throughout their chromosomes. By measuring these cells’ lengths and number of gene copies at the single‐cell level, we could fit a statistical model of the initiation and duration of chromosome replication. We found that for our slow‐growing (120 min doubling time) E. coli cells, replication was initiated 42 min into the cell cycle and completed after an additional 42 min. While simulations of the biogenesis model produce the correct ribosome and mRNA counts over the cell cycle, the kinetic parameters for transcription and degradation are lower than anticipated from a recent analytical time dependent model of in vivo mRNA production. Describing expression in terms of a simple chemical master equation, we show that the discrepancies are due to the lack of nonribosomal genes in the extended biogenesis model which effects the competition of mRNA for ribosome binding, and suggest corrections to parameters to be used in the whole‐cell model when modeling expression of the entire transcriptome. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 735–751, 2016.
Promoting convergence: The integrated graduate program in physical and engineering biology at Yale University, a new model for graduate education
Authors: Noble Dorottya B. , Mochrie Simon G. J. , O'Hern Corey S. , Pollard Thomas D. , Regan Lynne 
Published: June 2016

AbstractIn 2008, we established the Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) at Yale University. Our goal was to create a comprehensive graduate program to train a new generation of scientists who possess a sophisticated understanding of biology and who are capable of applying physical and quantitative methodologies to solve biological problems. Here we describe the framework of the training program, report on its effectiveness, and also share the insights we gained during its development and implementation. The program features co‐teaching by faculty with complementary specializations, student peer learning, and novel hands‐on courses that facilitate the seamless blending of interdisciplinary research and teaching. It also incorporates enrichment activities to improve communication skills, engage students in science outreach, and foster a cohesive program cohort, all of which promote the development of transferable skills applicable in a variety of careers. The curriculum of the graduate program is integrated with the curricular requirements of several Ph.D.‐granting home programs in the physical, engineering, and biological sciences. Moreover, the wide‐ranging recruiting activities of the IGPPEB serve to enhance the quality and diversity of students entering graduate school at Yale. We also discuss some of the challenges we encountered in establishing and optimizing the program, and describe the institution‐level changes that were catalyzed by the introduction of the new graduate program. The goal of this article is to serve as both an inspiration and as a practical “how to” manual for those who seek to establish similar programs at their own institutions. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):537–549, 2016.
Ginsenoside Rg1 inhibits angiotensin II‐induced podocyte autophagy via AMPK/mTOR/PI3K pathway
Authors: Mao Nan , Tan Rui‐Zhi , Wang Shao‐Qing , Wei Cong , Shi Xin‐Li , Fan Jun‐Ming , Wang Li 
Published: June 2016

AbstractRecent researches have reported the extensive pharmacological activities of Ginsenoside Rg1 including antioxidant, anti‐inflammatory, and anticancer properties. Furthermore Rg1 was also shown to protect various kinds of cells from self‐digestion by its anti‐autophagy activity. In previous studies, angiotensin II (Ang II), a key mediator of renin–angiotensin system, has been demonstrated to contribute to the progression of renal injury including abnormal autophagy. However, whether Rg1 can relieve Ang II‐induced autophagy in podocyte as well as the underlying molecular mechanism remains to be elucidated. Here, we employed Ang II‐treated podocyte as a model to investigate the effect of Rg1 on autophagy and the involved signal pathways. In the present study, we found that Ang II strongly promoted autophagy in immortalized mouse podocyte cells by observing the formation of autophagosomes and detecting the expression of autophagic marker, for example, LC3‐II. Notably, compared to the Ang II‐treated cells, treatment with Rg1 significantly inhibited the formation of autophagosomes and expression of autophagy‐related proteins in Ang II pre‐treated podocyte. Meanwhile, Rg1 downregulated the activity of AMPK and GSK‐3β and upregulated the activity of P70S6K in Ang II‐treated podocyte. In conclusion, these findings demonstrate that Ang II promotes autophagy in podocyte, and Rg1 effectively attenuates this process through AMPK/mTOR/PI3K pathway, suggesting that Rg1 may be beneficial to alleviate podocyte injury.
Reaction‐Kinetics‐Tuned Synthesis of Platinum Nanorods and Nanodendrites with Enhanced Electrocatalytic Performance for Oxygen Reduction
Authors: Xiong Xiaoli , Liao Yuxiang , Du Cheng , Luo Wei , Chen Shengli 
Published: June 2016

AbstractWe report a facile strategy to tune the growth behavior and surface structures of Pt nanocrystallites by varying the concentration of oleylamine (OAm) in mixed solutions of OAm and octadecene (ODE); the resulting Pt nanorods (NRs) and nanodendrites (NDs) show superior electrocatalytic performance for the oxygen reduction reaction (ORR). Long wormlike NRs with uniformly small diameters and NDs branched with NRs were obtained at low and medium concentrations of OAm, respectively. Time‐dependent morphology measurements showed that small Pt nanoparticles (NPs) were initially formed, which evolved into NRs or NDs depending on the reaction kinetics for Pt atom formation. Benefiting from the selective exposure of the ORR‐active (111) facet, the wormlike Pt NRs exhibited significantly higher ORR activity and electrochemical stability than state‐of‐the‐art Pt NP catalysts, which are enclosed with both the (111) and (100) facets. The ORR activity and stability of these catalysts were further enhanced by forming Pt NDs, probably as a result of the fact that the NR‐interconnected architectures produce more‐active high‐index facets in the junction areas.
Linear Optical and Third‐Order Nonlinear Optical Properties of Some Fluorenyl‐ and Triarylamine‐Containing Tetracyanobutadiene Derivatives
Authors: Pokladek Ziemowit , Ripoche Nicolas , Betou Marie , Trolez Yann , Mongin Olivier , Olesiak‐Banska Joanna , Matczyszyn Katarzyna , Samoc Marek , Humphrey Mark G. , Blanchard‐Desce Mireille , Paul Frédéric 
Published: June 2016

AbstractThe synthesis and characterization of four new tetracyanobutadiene (TCBD) derivatives (1–3 and 2′) incorporating 2‐ or 2,7‐fluorenyl and diphenylamino moieties are reported. The electroactivity of 1–3 and 2′ was studied by cyclic voltammetry (CV), while the linear optical and (third‐order) nonlinear optical (NLO) properties were investigated by electronic spectroscopy and Z‐scan studies, respectively. All experimental investigations were rationalized by DFT computations, providing an insight into the electronic structure of these derivatives and on their application potential. We show that these derivatives are nonluminescent in solution at ambient temperatures, but become fluorescent in solvent glasses. This finding constitutes an unprecedented observation for TCBD derivatives. Also, we show by Z‐scan studies that these derivatives behave as two‐photon absorbers in the near‐IR range (800–1050 nm). These third‐order NLO properties are discussed and compared with those of their alkynyl precursors (4–6), which have been investigated by two‐photon excited fluorescence (TPEF).
Triptycene‐Based Chiral and meso‐N‐Heterocyclic Carbene Ligands and Metal Complexes
Authors: Savka Roman , Bergmann Marvin , Kanai Yuki , Foro Sabine , Plenio Herbert 
Published: June 2016

AbstractBased on 1‐amino‐4‐hydroxy‐triptycene, new saturated and unsaturated triptycene‐NHC (N‐heterocyclic carbene) ligands were synthesized from glyoxal‐derived diimines. The respective carbenes were converted into metal complexes [(NHC)MX] (M=Cu, Ag, Au; X=Cl, Br) and [(NHC)MCl(cod)] (M=Rh, Ir; cod=1,5‐cyclooctadiene) in good yields. The new azolium salts and metal complexes suffer from limited solubility in common organic solvents. Consequently, the introduction of solubilizing groups (such as 2‐ethylhexyl or 1‐hexyl by O‐alkylation) is essential to render the complexes soluble. The triptycene unit infers special steric properties onto the metal complexes that enable the steric shielding of selected areas close to the metal center. Next, chiral and meso‐triptycene based N‐heterocyclic carbene ligands were prepared. The key step in the synthesis of the chiral ligand is the Buchwald–Hartwig amination of 1‐bromo‐4‐butoxy‐triptycene with (1S,2S)‐1,2‐diphenyl‐1,2‐diaminoethane, followed by cyclization to the azolinium salt with HC(OEt)3. The analogous reaction with meso‐1,2‐diphenyl‐1,2‐diaminoethane provides the respective meso‐azolinium salt. Both the chiral and meso‐azolinium salts were converted into metal complexes including [(NHC)AuCl], [(NHC)RhCl(cod)], [(NHC)IrCl(cod)], and [(NHC)PdCl(allyl)]. An in situ prepared chiral copper complex was tested in the enantioselective borylation of α,β‐unsaturated esters and found to give an excellent enantiomeric ratio (er close to 90:10).
Specific Design of Titanium(IV) Phenolato Chelates Yields Stable and Accessible, Effective and Selective Anticancer Agents
Authors: Meker Sigalit , Braitbard Ori , Hall Matthew D. , Hochman Jacob , Tshuva Edit Y. 
Published: June 2016

AbstractInvited for the cover of this issue is the group of Edit Y. Tshuva at The Hebrew University of Jerusalem and co‐workers. The image depicts a phenolato titanium(IV) complex as the Joker that combines four qualities essential for an anticancer drug: stability, efficacy, accessibility and selectivity. Read the full text of the article at 10.1002/chem.201601389.
Boundary Value Problems for Second‐Order Elliptic Operators Satisfying a Carleson Condition
Authors: Dindoš Martin , Pipher Jill , Rule David 
Published: June 2016

AbstractLet Ω be a Lipschitz domain in , and be a second‐order elliptic operator in divergence form. We establish the solvability of the Dirichlet regularity problem with boundary data in and of the Neumann problem with data for the operator L on Lipschitz domains with small Lipschitz constant. We allow the coefficients of the operator L to be rough, obeying a certain Carleson condition with small norm. These results complete the results of Dindoš, Petermichl, and Pipher (2007), where the Dirichlet problem was considered under the same assumptions, and Dindoš and Rule (2010), where the regularity and Neumann problems were considered on two‐dimensional domains.© 2016 Wiley Periodicals, Inc.
The Antinociceptive Effects of Tramadol and/or Gabapentin on Rat Neuropathic Pain Induced by a Chronic Constriction Injury
Authors: Corona‐Ramos Janette Nallely , De la O‐Arciniega Minarda , Déciga‐Campos Myrna , Medina‐López José Raúl , Domínguez‐Ramírez Adriana Miriam , Jaramillo‐Morales Osmar Antonio , Espinosa‐Juárez Josué Vidal , López‐Muñoz Francisco Javier 
Published: June 2016

Abstract

Preclinical Research

The current work evaluates the interaction between two commonly used drugs, tramadol (Tra) and gabapentin (Gbp). Dose‐response curves (DRC) and isobolographic analysis were used to confirm their synergistic antihyperalgesic and anti‐allodynic responses in a rat neuropathic pain model involving chronic constriction injury of the sciatic nerve and in von Frey and acetone tests. Tra and Gbp produced dose‐dependent antihyperalgesic and anti‐allodynic effects. Dose‐response studies of combinations of Tra and Gbp in combination showed the DRC was leftward‐shifted compared to the DRCs for each compound alone. One combination demonstrated both antihyperalgesic and anti‐allodynic effects greater than those observed after individual administration. The remaining combinations demonstrated an additive effect. The Tra+Gbp combination demonstrated a potentiative effect with smaller doses of Tra. Additionally, it was determined lethal dose 50 (LD50) of Tra alone and tramadol + Gbp 10 using mice to 48 h post administration. The DRC (death) were similar for Tra alone and in Tra in combination, despite the improved effectiveness of Tra in the presence of GBP, 10 mg/kg. A combination of these drugs could be effective in neuropathic pain therapy because they can produce potentiative (at a low dose) or additive effects. Drug Dev Res 77 : 217–226, 2016.   © 2016 Wiley Periodicals, Inc.
Dietary choice for a balanced nutrient intake increases the mean and reduces the variance in the reproductive performance of male and female cockroaches
Authors: Bunning Harriet , Bassett Lee , Clowser Christina , Rapkin James , Jensen Kim , House Clarissa M. , Archer Catharine R. , Hunt John 
Published: June 2016

AbstractSexual selection may cause dietary requirements for reproduction to diverge across the sexes and promote the evolution of different foraging strategies in males and females. However, our understanding of how the sexes regulate their nutrition and the effects that this has on sex‐specific fitness is limited. We quantified how protein (P) and carbohydrate (C) intakes affect reproductive traits in male (pheromone expression) and female (clutch size and gestation time) cockroaches (Nauphoeta cinerea). We then determined how the sexes regulate their intake of nutrients when restricted to a single diet and when given dietary choice and how this affected expression of these important reproductive traits. Pheromone levels that improve male attractiveness, female clutch size and gestation time all peaked at a high daily intake of P:C in a 1:8 ratio. This is surprising because female insects typically require more P than males to maximize reproduction. The relatively low P requirement of females may reflect the action of cockroach endosymbionts that help recycle stored nitrogen for protein synthesis. When constrained to a single diet, both sexes prioritized regulating their daily intake of P over C, although this prioritization was stronger in females than males. When given the choice between diets, both sexes actively regulated their intake of nutrients at a 1:4.8 P:C ratio. The P:C ratio did not overlap exactly with the intake of nutrients that optimized reproductive trait expression. Despite this, cockroaches of both sexes that were given dietary choice generally improved the mean and reduced the variance in all reproductive traits we measured relative to animals fed a single diet from the diet choice pair. This pattern was not as strong when compared to the single best diet in our geometric array, suggesting that the relationship between nutrient balancing and reproduction is complex in this species.
Identification of Linear Time‐Invariant Systems under Periodic Disturbance with Its Estimation
Authors: KANEKO OSAMU , OHMURA KAZUKI , HAYASHI YUUKI , YAMAMOTO SHIGERU 
Published: June 2016

SUMMARYIn this paper, we propose a new method for identification of linear time‐invariant systems and estimation of unknown periodic disturbances. We assume that a disturbance to be considered here is unknown except its period. In this method, by stacking not only the unknown coefficients of a mathematical model but also the unknown disturbance as a parameter vector, we modify the equation error method so as to treat the unknown disturbance in the identification scheme. In particular, we also explain how the periodicity of the disturbance is utilized. In order to show the validity of this method, we give an illustrative numerical example.
Myocardial recovery with mechanical circulatory support
Authors: Chaggar Parminder S. , Williams Simon G. , Yonan Nizar , Fildes James , Venkateswaran Rajamiyer , Shaw Steven M. 
Published: June 2016

AbstractMechanical circulatory support (MCS) is instituted in patients with advanced heart failure, some of who may experience sufficient recovery in cardiac function to allow withdrawal of mechanical support. The incidence of left ventricular recovery with MCS is unclear as reported series in the literature demonstrate widely divergent rates. A number of clinical parameters (including echocardiographic, haemodynamic and physiological) are used to indicate likely left ventricular recovery during pump speed reduction but no internationally agreed definition exists. Withdrawal of MCS is not without risk and so robust clinical and biochemical definitions are important to minimize patient morbidity and mortality. Here we review our current understanding of left ventricular recovery with MCS.
Study on Determinants of Chinese Managers’ Crisis Intention under Financial Turbulence: An Empirical Study Based on Chinese Listed Companies
Authors: Sheng Zhonglin , He Weida 
Published: June 2016

AbstractThis article presents a study on determinants of Chinese managers’ crisis intention under the global financial turbulence from a resource‐based view. It draws three important findings through an empirical analysis of 91 Chinese listed companies. First, there is a significant negative relationship between slack resources and crisis intention. Second, there is a significant positive relationship between diversification and crisis intention. Finally, diversification positively moderates the linkage between slack resources and crisis intention. This study extends the resource‐based view to the area of crisis
management and provides important guidance on how to effectively deal with the current
economic crisis.
Characterization of a Relatively Malignant Form of Osteopetrosis Caused by a Novel Mutation in the PLEKHM1 Gene
Authors: Bo Tao , Yan Fang , Guo Jun , Lin Xiaoyan , Zhang Haiqing , Guan Qingbo , Wang Hai , Fang Li , Gao Ling , Zhao Jiajun , Xu Chao 
Published: June 2016

ABSTRACT

Osteopetrosis (OMIM: 611497), literally “stone bone,” is a group of inherited bone disorders characterized by increased skeletal mass due to defective osteoclast function. A patient who reported a history of frequent fractures, weakness and fatigue was admitted to our hospital in 2011. The patient presented with the typical features of osteopetrosis: fractures after minor trauma, early tooth loss, anemia, hepatosplenomegaly, and a generalized increase in bone mineral density (BMD). Aside from his father's complaint of excessive tooth loss, his mother, two sisters, son, and daughter were healthy. Blood samples of the family members were drawn for genetic analyses. The entire coding region and adjacent splice sites of the pleckstrin homology domain–containing family M (with RUN domain) member 1 (PLEKHM1) gene were sequenced. One mutation, a heterozygous deletion mutation in exon 11 (c.3051_3052delCA), was identified in the patient but not in his relatives. The mutation leads to a translation product with a highly impaired Rubicon homology domain. Co-immunoprecipitation and immunofluorescence analyses using HEK293 cells showed that overexpression of a PLEKHM1 CA-deletion mutant resulted in a dramatic decrease in the interaction between PLEKHM1 and the small GTPase Rab7 compared to wild-type PLEKHM1. The normal processes of endocytosis and autophagy were disturbed in cells expressing the mutant (transfected HEK293 and U937 cells), as indicated by epidermal growth factor receptor (EGFR) degradation and an altered LC3-I/II ratio, respectively, which may lead to a defect in osteoclast function. A four-year follow-up study of the patient showed that the PLEKHM1-dependent osteopetrosis was relatively malignant, with significant symptoms of pancytopenia and hepatosplenomegaly. © 2016 American Society for Bone and Mineral Research.
Suppression of Spleen Tyrosine Kinase (Syk) by Histone Deacetylation Promotes, Whereas BAY61‐3606, a Synthetic Syk Inhibitor Abrogates Colonocyte Apoptosis by ERK Activation
Authors: Dasgupta Nirmalya , Thakur Bhupesh Kumar , Ta Atri , Dutta Pujarini , Das Santasabuj 
Published: June 2016

ABSTRACTSpleen tyrosine kinase (Syk), a non‐receptor tyrosine kinase, regulates tumor progression, either negatively or positively, depending on the tissue lineage. Information about the role of Syk in colorectal cancers (CRC) is limited, and conflicting reports have been published. We studied Syk expression and its role in differentiation and apoptosis of the colonocytes. Here, we reported for the first time that expression of two transcript variants of Syk is suppressed in colonocytes during butyrate‐induced differentiation, which mediates apoptosis of HT‐29 cells. Despite being a known HDAC inhibitor, butyrate deacetylates histone3/4 around the transcription start site (TSS) of Syk. Histone deacetylation precludes the binding of RNA Polymerase II to the promoter and inhibits transcription. Since butyrate is a colonic metabolite derived from undigested fibers, our study offers a plausible explanation of the underlying mechanisms of the protective role of butyrate as well as the dietary fibers against CRC through the regulation of Syk. We also report that combined use of butyrate and highly specific Syk inhibitor BAY61‐3606 does not enhance differentiation and apoptosis of colonocytes. Instead, BAY completely abolishes butyrate‐induced differentiation and apoptosis in a Syk‐ and ERK1/2‐dependent manner. While butyrate dephosphorylates ERK1/2 in HT‐29 cells, BAY re‐phosphorylates it, leading to its activation. This study describes a novel mechanism of butyrate action in CRC and explores the role of Syk in butyrate‐induced differentiation and apoptosis. In addition, our study highlights those commercial small molecule inhibitors, although attractive drug candidates should be used with concern because of their frequent off‐target effects. J. Cell. Biochem. 118: 191–203, 2017. © 2016 Wiley Periodicals, Inc.
Even Embeddings of the Complete Graphs and Their Cycle Parities
Authors: Noguchi Kenta 
Published: June 2016

AbstractThe complete graph on n vertices can be quadrangularly embedded on an orientable (resp. nonorientable) closed surface F2 with Euler characteristic if and only if (resp. and ). In this article, we shall show that if quadrangulates a closed surface F2, then has a quadrangular embedding on F2 so that the length of each closed walk in the embedding has the parity specified by any given homomorphism , called the cycle parity.
Matching Extension Missing Vertices and Edges in Triangulations of Surfaces
Authors: Kawarabayashi Ken‐ichi , Ozeki Kenta , Plummer Michael D. 
Published: June 2016

AbstractLet G be a 5‐connected triangulation of a surface Σ different from the sphere, and let be the Euler characteristic of Σ. Suppose that with even and M and N are two matchings in of sizes m and n respectively such that . It is shown that if the pairwise distance between any two elements of is at least five and the face‐width of the embedding of G in Σ is at least , then there is a perfect matching M0 in containing M such that .