bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of subunit assembly and function of the Saccharomyces cerevisiae RNase H2 complex
Authors: Nguyen Tuan Anh , Tak Yon‐Soo , Lee Chul‐Hwan , Kang Young‐Hoon , Cho Il‐Taeg , Seo Yeon‐Soo 
Published: October 2011

RNase H2 of Saccharomyces cerevisiae consists of three essential subunits (Rnh201, Rnh202 and Rnh203) and plays a critical role in the removal of RNA incorporated in duplex DNA. In the present study, we purified individual subunits and heterodimeric subcomplexes to examine the assembly and biochemical function of subunits of RNase H2 in vitro. Reconstitution experiments revealed that Rnh202 and Rnh203 first form a subcomplex, followed by the recruitment of Rnh201 to complete complex formation. Rnh201 alone or in combination with Rnh203 showed neither substrate‐binding, nor catalytic activity, indicating that both activities of Rnh201 are latent until it becomes an integral part of the complex. However, Rnh202 by itself showed substrate‐binding activity. RNase H2 containing mutant Rnh202 defective in substrate binding had decreased substrate‐binding activity, indicating that Rnh202 contributes directly to substrate binding. Reconstitution of RNase H2 complexes with various mutant subunits allowed us to assess the influence of conserved amino acid residues in either Rnh201 or Rnh202 on substrate‐binding and catalytic activities. We found that the substrate‐binding activities of both Rnh201 and Rnh202 were critical for cleavage of the phosphodiester bond present between DNA and RNA in RNase H2 substrates.Structured digital abstract
RNH202 physically interacts with RNH201 by pull down (View interaction)
RNH201 binds to RNH203 by pull down (View interaction)
RNH202 binds to RNH203 by pull down (View interaction)
Rate, affinity and calcium dependence of nitric oxide synthase isoform binding to the primary physiological regulator calmodulin
Authors: McMurry Jonathan L. , Chrestensen Carol A. , Scott Israel M. , Lee Elijah W. , Rahn Aaron M. , Johansen Allan M. , Forsberg Brian J. , Harris Kyle D. , Salerno John C. 
Published: October 2011

Using interferometry‐based biosensors the binding and release of endothelial and neuronal nitric oxide synthase (eNOS and nNOS) from calmodulin (CaM) was measured. In both isoforms, binding to CaM is diffusion limited and within approximately three orders of magnitude of the Smoluchowski limit imposed by orientation‐independent collisions. This suggests that the orientation of CaM is facilitated by the charge arrays on the CaM‐binding site and the complementary surface on CaM. Protein kinase C phosphorylation of eNOS T495, adjacent to the CaM‐binding site, abolishes or greatly slows CaM binding. Kinases which increase the activity of eNOS did not stimulate the binding of CaM, which is already diffusion limited. The coupling of Ca2+ binding and CaM/NOS binding equilibria links the affinity of CaM for NOS to the Ca2+ dependence of CaM binding. Hence, changes in the Ca2+ sensitivity of CaM binding always imply changes in the NOS–CaM affinity. It is possible, however, that in some regimes binding and activation are not synonymous, so that Ca2+ sensitivity need not be tightly linked to CaM sensitivity of activation. This study is being extended using mutants to probe the roles of individual structural elements in binding and release.Structured digital abstract
CaM binds to eNOS by biophysical (View interaction)
CaM binds to nNOS by biophysical (View interaction)
eNOS binds to CaM by biophysical (View interaction)
Photophysical diversity of two novel cyanobacteriochromes with phycocyanobilin chromophores: photochemistry and dark reversion kinetics
Authors: Chen Yu , Zhang Juan , Luo Juan , Tu Jun‐Ming , Zeng Xiao‐Li , Xie Jie , Zhou Ming , Zhao Jing‐Quan , Scheer Hugo , Zhao Kai‐Hong 
Published: October 2011

Cyanobacteriochromes are phytochrome homologues in cyanobacteria that act as sensory photoreceptors. We compare two cyanobacteriochromes, RGS (coded by slr1393) from Synechocystis sp. PCC 6803 and AphC (coded by all2699) from Nostoc sp. PCC 7120. Both contain three GAF (cGMP phosphodiesterase, adenylyl cyclase and FhlA protein) domains (GAF1, GAF2 and GAF3). The respective full‐length, truncated and cysteine point‐mutated genes were expressed in Escherichia coli together with genes for chromophore biosynthesis. The resulting chromoproteins were analyzed by UV‐visible absorption, fluorescence and circular dichroism spectroscopy as well as by mass spectrometry. RGS shows a red–green photochromism (λmax = 650 and 535 nm) that is assigned to the reversible 15Z/E isomerization of a single phycocyanobilin‐chromophore (PCB) binding to Cys528 of GAF3. Of the three GAF domains, only GAF3 binds a chromophore and the binding is autocatalytic. RGS autophosphorylates in vitro; this reaction is photoregulated: the 535 nm state containing E‐PCB was more active than the 650 nm state containing Z‐PCB. AphC from Nostoc could be chromophorylated at two GAF domains, namely GAF1 and GAF3. PCB‐GAF1 is photochromic, with the proposed 15E state (λmax = 685 nm) reverting slowly thermally to the thermostable 15Z state (λmax = 635 nm). PCB‐GAF3 showed a novel red–orange photochromism; the unstable state (putative 15E, λmax = 595 nm) reverts very rapidly (τ∼ 20 s) back to the thermostable Z state (λmax = 645 nm). The photochemistry of doubly chromophorylated AphC is accordingly complex, as is the autophosphorylation: E‐GAF1/E‐GAF3 shows the highest rate of autophosphorylation activity, while E‐GAF1/Z‐GAF3 has intermediate activity, and Z‐GAF1/Z‐GAF3 is the least active state.Structured digital abstract
AphC phosphorylates AphC  by protein kinase assay (View interaction)
RGS phosphorylates RGS  by protein kinase assay (View interaction)
Identification of Dp71e, a new dystrophin with a novel carboxy‐terminal end
Authors: Saint Martín Abril , Aragón Jorge , Depardon‐Benítez Francisco , Sánchez‐Trujillo Alejandra , Mendoza‐Hernández Guillermo , Ceja Victor , Montañez Cecilia 
Published: October 2011

Several dystrophin Dp71 isoforms have previously been described and can be grouped into two subfamilies (Dp71d or Dp71f) depending upon the splicing of exon 78. As a consequence of this splicing, each group has a carboxy‐terminal end with a unique amino acid composition; this composition imparts specific characteristics with respect to subcellular localization and interactions with particular members of the dystrophin‐associated proteins (DAPs) complex. We have discovered a new alternative splicing event at the 3′ region of the Dp71 transcript. This spliced region has a unique sequence that codes for 10 amino acids and prevents the translation of exons 78 and 79. This novel Dp71 isoform is called Dp71e and is expressed in undifferentiated cells and during nerve growth factor‐induced differentiation of PC12 cells. Interestingly, Dp71e mRNA and protein expression increase during PC12 cell differentiation mediated by NGF. This new Dp71 isoform is also expressed in rat organs and in human cell lines.Database
Dp71e nucleotide sequence data are available in the GenBank/EMBL/DDBJ databases under the accession number JF510048.1
Role of charged residues in stabilization of Pyrococcus horikoshii CutA1, which has a denaturation temperature of nearly 150 °C
Authors: Matsuura Yoshinori , Takehira Michiyo , Sawano Masahide , Ogasahara Kyoko , Tanaka Tomoyuki , Yamamoto Hitoshi , Kunishima Naoki , Katoh Etsuko , Yutani Katsuhide 
Published: October 2011

The CutA1 protein from Pyrococcus horikoshii (PhCutA1), a hyperthermophile, has an unusually high content of charged residues and an unusually high denaturation temperature. To elucidate the role of ion–ion interactions in protein stability, mutant proteins of PhCutA1 in which charged residues were substituted by noncharged residues were comprehensively examined. The denaturation temperatures (Td) for 13 of 53 examined mutant proteins were higher than that of the wild‐type (148.5 °C at pH 7.0), among which E99Q had the highest Td at 154.9 °C. R25A had the largest decrease in Td among single mutants at ΔTd = −12.4 °C. The average decrease in Td of Lys or Arg mutants was greater than that of Glu or Asp mutants, and the average change in Td (ΔTd) of 21 Glu mutants was negligible, at 0.03 ± 2.05 °C. However, the electrostatic energy (−159.3 kJ·mol−1) of PhCutA1 was quite high, compared with that of CutA1 from Escherichia coli (−9.7 kJ·mol−1), a mesophile. These results indicate that: (a) many Glu and Asp residues of PhCutA1 should be essential for highly efficient interactions with positively charged residues and for generating high electrostatic energy, although they were forced to be partially repulsive to each other; (b) the changes in stability of mutant proteins with a Td value of ∼ 140–150 °C were able to be explained by considering factors important for protein stability and the structural features of mutant sites; and (c) these findings are useful for the design of proteins that are stable at temperatures > 100 °C.Database
Structural data are available from the Protein Data Bank under the accession codes for 1v99 and 1naq of CutA1 proteins from P. Horikoshii and E. coli, respectively
The Effectiveness of Ozone and Acidulant Treatments in Extending the Refrigerated Shelf Life of Fresh‐Cut Potatoes
Authors: Calder Beth L. , Skonberg Denise I. , Davis‐Dentici Katherine , Hughes Brianna H. , Bolton Jason C. 
Published: October 2011

Abstract:  The objective of the study was to determine the effectiveness of acidulant dip treatments (with or without aqueous ozone) to reduce enzymatic browning and to extend the shelf life of fresh‐cut potato slices during refrigerated storage (4 °C) for 28 d. Potato slices subjected to aqueous ozone (2 ppm) had significantly (P≤ 0.05) higher L‐values and lower a‐values, but ozone did not appear to have any effect on aerobic plate counts (APCs) or polyphenol oxidase (PPO) activity. NatureSeal (NS) and sodium acid sulfate (SAS) were the most effective acidulant treatments in reducing browning (significantly [P≤ 0.05] higher L‐values, lower a‐values, and browning index values) regardless of ozone treatment. NS and SAS also had lower PPO activity compared to other treatments on days 0 and 28, and significantly (P≤ 0.05) lower APCs (≤2.00 log CFU/g) over refrigerated storage. Therefore, the SAS treatment was comparable to NS, a commercially available product, and showed promise as an effective antibrowning dip to reduce browning and spoilage in fresh‐cut potato products.Practical Application:  A 1% SAS dip treatment which included 1% citric and 1% ascorbic acid was found to be an effective antibrowning dip for fresh‐cut potatoes along with NatureSeal®'s PS‐10, compared to other treatments. They were both effective in maintaining low microbial counts over refrigerated storage. Additionally, aqueous ozone washes (2 ppm) showed significant benefits to reduce browning; however, ozone did not affect microbial counts or PPO enzyme activity. Therefore, the SAS treatment could have potential use in the fruit and vegetable industry to reduce browning and spoilage in fresh‐cut potato products.
Not So Bad After All: How Relational Closeness Buffers the Association Between Relationship Conflict and Helpful and Deviant Group Behaviors
Authors: Rispens Sonja , Greer Lindred , Jehn Karen A. , Thatcher Sherry M. B. 
Published: October 2011

AbstractPast research has left unanswered the question of how to reduce the negative effects of relationship conflict in work groups. This study investigates whether relational closeness in work groups buffers the negative association between relationship conflict and two important group behaviors that are often overlooked in conflict research: group‐level helping behavior and counterproductive work behavior. The results of this field study show that the degree of relational closeness in work groups indeed buffers the negative affiliation between relationship conflict and group‐level helping behavior and the positive association between relationship conflict and group‐level counterproductive work behavior. Specifically, the results suggest that relationship conflicts are only harmful in relationally distant work groups in which members do not know each other well personally and do not feel close to each other. Theoretical implications and suggestions for organizational practice are discussed.
Grazing impacts on Auchenorrhyncha diversity and abundance on a Scottish upland estate
Authors: LITTLEWOOD NICK A. , PAKEMAN ROBIN J. , POZSGAI GABOR 
Published: October 2011

Abstract.  1. Livestock grazing impacts on insect populations in a variety of ways. For phytophagous insects the impact is primarily a result of altering the structure and species assemblage of vegetation. However not all species react in similar ways and even within an order there may be winners and losers from different grazing regimes.2. A long‐term, replicated, controlled experiment, comprising four grazing treatments, was established within an upland acid grassland area in Scotland. Auchenorrhyncha were sampled by suction sampling and sweep‐netting in the fifth year following the start of the treatments.3. A significant treatment effect was apparent in the suction samples with Auchenorrhyncha abundance being three to four times higher in the ungrazed plots compared to the other treatments. Abundance was also highest from the ungrazed plots in the sweep net samples, but this effect was not statistically significant. Redundancy analysis (RDA) showed that a suite of species which are typical of shaded positions responded with increased abundance in the ungrazed plots.4. The findings demonstrate that the assemblages found in ungrazed areas can be vastly different to those found in even lightly grazed areas and therefore, underline the benefits of varied grazing regimes in maximising diversity. Furthermore, the work underlines the benefit of employing multiple sampling methods.
Geomycology: metals, actinides and biominerals
Authors: Gadd Geoffrey Michael , Rhee Young Joon , Stephenson Karen , Wei Zhan 
Published: October 2011

SummaryGeomycology can be simply defined as ‘the scientific study of the roles of fungi in processes of fundamental importance to geology’ and the biogeochemical importance of fungi is significant in several key areas. These include nutrient and element cycling, rock and mineral transformations, bioweathering, mycogenic biomineral formation and interactions of fungi with clay minerals and metals. Such processes can occur in aquatic and terrestrial habitats, but it is in the terrestrial environment where fungi probably have the greatest geochemical influence. Of special significance are the mutualistic relationships with phototrophic organisms, lichens (algae, cyanobacteria) and mycorrhizas (plants). Central to many geomycological processes are transformations of metals and minerals, and fungi possess a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Some fungal transformations have beneficial applications in environmental biotechnology, e.g. in metal and radionuclide leaching, recovery, detoxification and bioremediation, and in the production or deposition of biominerals or metallic elements with catalytic or other properties. Metal and mineral transformations may also result in adverse effects when these processes result in spoilage and destruction of natural and synthetic materials, rock and mineral‐based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment. The ubiquity and importance of fungi in biosphere processes underlines the importance of geomycology as an interdisciplinary subject area within microbiology and mycology.
Microstructure Characterization of Simulated Tri‐Isotropic Particles Embedded in Alkaline Borosilicate Glass
Authors: Hamodi Nasir H. , Abram Timothy J. 
Published: October 2011

A preliminary study of the encapsulation of tri‐isotropic (TRISO) coated particles in alkaline borosilicate glass (ABG) using melting and casting methods is presented. ABG has been developed to encapsulate simulated TRISO fuel particles that are used as nuclear fuel elements in Very High Temperature Reactors. Encapsulation is an alternative to vitrification and it is a process in which radioactive waste is encapsulated within a composite as a first barrier and a glass matrix as a second barrier. This provides two barriers against leaching and diffusion of the radioactive waste once buried in the geological repository. The study investigates the possibility of achieving high densification of glass–graphite composite by sealing the pores of TRISO particles surrogate (28 wt% CeO2, 70 wt% graphite, and 2 wt% poly‐ethylene glycol) with molten ABG at 600°C. This article follows the carbon phases during the encapsulation and highlights the interaction area between the carbon and glass phases before and after melting, using a polarized laser source (Ar, 514 nm). The laser analysis revealed that the graphite no longer was retained in graphene hexagonal structure and that it was linked with the glass network as disordered carbon atoms.
Image quality improvement in megavoltage cone beam CT using an imaging beam line and a sintered pixelated array system
Authors: Breitbach Elizabeth K. , Maltz Jonathan S. , Gangadharan Bijumon , Bani‐Hashemi Ali , Anderson Carryn M. , Bhatia Sudershan K. , Stiles Jared , Edwards Drake S. , Flynn Ryan T. 
Published: October 2011

Purpose:To quantify the improvement in megavoltage cone beam computed tomography (MVCBCT) image quality enabled by the combination of a 4.2 MV imaging beam line (IBL) with a carbon electron target and a detector system equipped with a novel sintered pixelated array (SPA) of translucent Gd2O2S ceramic scintillator. Clinical MVCBCT images are traditionally acquired with the same 6 MV treatment beam line (TBL) that is used for cancer treatment, a standard amorphous Si (a‐Si) flat panel imager, and the Kodak Lanex Fast‐B (LFB) scintillator. The IBL produces a greater fluence of keV‐range photons than the TBL, to which the detector response is more optimal, and the SPA is a more efficient scintillator than the LFB.Methods:A prototype IBL + SPA system was installed on a Siemens Oncor linear accelerator equipped with the MVisionTM image guided radiation therapy (IGRT) system. A SPA strip consisting of four neighboring tiles and measuring 40 cm by 10.96 cm in the crossplane and inplane directions, respectively, was installed in the flat panel imager. Head‐ and pelvis‐sized phantom images were acquired at doses ranging from 3 to 60 cGy with three MVCBCT configurations: TBL + LFB, IBL + LFB, and IBL + SPA. Phantom image quality at each dose was quantified using the contrast‐to‐noise ratio (CNR) and modulation transfer function (MTF) metrics. Head and neck, thoracic, and pelvic (prostate) cancer patients were imaged with the three imaging system configurations at multiple doses ranging from 3 to 15 cGy. The systems were assessed qualitatively from the patient image data.Results:For head and neck and pelvis‐sized phantom images, imaging doses of 3 cGy or greater, and relative electron densities of 1.09 and 1.48, the CNR average improvement factors for imaging system change of TBL + LFB to IBL + LFB, IBL + LFB to IBL + SPA, and TBL + LFB to IBL + SPA were 1.63 (p < 10− 8), 1.64 (p < 10− 13), 2.66 (p < 10− 9), respectively. For all imaging doses, soft tissue contrast was more easily differentiated on IBL + SPA head and neck and pelvic images than TBL + LFB and IBL + LFB. IBL + SPA thoracic images were comparable to IBL + LFB images, but less noisy than TBL + LFB images at all imaging doses considered. The mean MTFs over all imaging doses were comparable, at within 3%, for all imaging system configurations for both the head‐ and pelvis‐sized phantoms.Conclusions:Since CNR scales with the square root of imaging dose, changing from TBL + LFB to IBL + LFB and IBL + LFB to IBL + SPA reduces the imaging dose required to obtain a given CNR by factors of 0.38 and 0.37, respectively. MTFs were comparable between imaging system configurations. IBL + SPA patient image quality was always better than that of the TBL + LFB system and as good as or better than that of the IBL + LFB system, for a given dose.
Ultrashort Peptide Bioconjugates Are Exclusively Antifungal Agents and Synergize with Cyclodextrin and Amphotericin B
Authors: Arnusch Christopher J. , Ulm Hannah , Josten Michaele , Shadkchan Yana , Osherov Nir , Sahl Hans-Georg , Shai Yechiel 
Published: October 2011

ABSTRACT

Many natural broad-spectrum cationic antimicrobial peptides (AMPs) possess a general mode of action that is dependent on lipophilicity and charge. Modulating the lipophilicity of AMPs by the addition of a fatty acid has been an effective strategy to increase the lytic activity and can further broaden the spectrum of AMPs. However, lipophilic modifications that narrow the spectrum of activity and exclusively direct peptides to fungi are less common. Here, we show that short peptide sequences can be targeted to fungi with structured lipophilic biomolecules, such as vitamin E and cholesterol. The conjugates were active against
Aspergillus fumigatus
,
Cryptococcus neoformans
, and
Candida albicans
but not against bacteria and were observed to cause membrane perturbation by transmission electron microscopy and in membrane permeability studies. However, for
C. albicans
, selected compounds were effective without the perturbation of the cell membrane, and synergism was seen with a vitamin E conjugate and amphotericin B. Moreover, in combination with β-cyclodextrin, antibacterial activity emerged in selected compounds. Biocompatibility for selected active compounds was tested
in vitro
and
in vivo
using toxicity assays on erythrocytes, macrophages, and mice.
In vitro
cytotoxicity experiments led to selective toxicity ratios (50% lethal concentration/MIC) of up to 64 for highly active antifungal compounds, and no
in vivo
murine toxicity was seen. Taken together, these results highlight the importance of the conjugated lipophilic structure and suggest that the modulation of other biologically relevant peptides with hydrophobic moieties, such as cholesterol and vitamin E, generate compounds with unique bioactivity.