bluuebunny/crossref_metadata_2025_split huggingface dataset:
Class III phosphatidylinositol 3–kinase and its catalytic product PtdIns3P in regulation of endocytic membrane traffic
Authors: Raiborg Camilla , Schink Kay O. , Stenmark Harald 
Published: January 2013

Endocytosis and subsequent membrane traffic through endosomes are cellular processes that are integral to eukaryotic evolution, and numerous human diseases are associated with their dysfunction. Consequently, it is important to untangle the molecular machineries that regulate membrane dynamics and protein flow in the endocytic pathway. Central in this context is class III phosphatidylinositol 3–kinase, an evolutionarily conserved enzyme complex that phosphorylates phosphatidylinositol into phosphatidylinositol 3–phosphate. Phosphatidylinositol 3–phosphate recruits specific effector proteins, most of which contain FYVE or PX domains, to promote endocytosis, endosome fusion, endosome motility and endosome maturation, as well as cargo sorting to lysosomes, the biosynthetic pathway or the plasma membrane. Here we review the functions of key phosphatidylinositol 3–phosphate effectors in regulation of endocytic membrane dynamics and protein sorting.
Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.)
Authors: Zhang Ji‐Yi , Lee Yi‐Ching , Torres‐Jerez Ivone , Wang Mingyi , Yin Yanbin , Chou Wen‐Chi , He Ji , Shen Hui , Srivastava Avinash C. , Pennacchio Christa , Lindquist Erika , Grimwood Jane , Schmutz Jeremy , Xu Ying , Sharma Manoj , Sharma Rita , Bartley Laura E. , Ronald Pamela C. , Saha Malay C. , Dixon Richard A. , Tang Yuhong , Udvardi Michael K. 
Published: January 2013

SummarySwitchgrass (Panicum virgatum L.) is a perennial C4 grass with the potential to become a major bioenergy crop. To help realize this potential, a set of RNA‐based resources were developed. Expressed sequence tags (ESTs) were generated from two tetraploid switchgrass genotypes, Alamo AP13 and Summer VS16. Over 11.5 million high‐quality ESTs were generated with 454 sequencing technology, and an additional 169 079 Sanger sequences were obtained from the 5′ and 3′ ends of 93 312 clones from normalized, full‐length‐enriched cDNA libraries. AP13 and VS16 ESTs were assembled into 77 854 and 30 524 unique transcripts (unitranscripts), respectively, using the Newbler and pave programs. Published Sanger‐ESTs (544 225) from Alamo, Kanlow, and 15 other cultivars were integrated with the AP13 and VS16 assemblies to create a universal switchgrass gene index (PviUT1.2) with 128 058 unitranscripts, which were annotated for function. An Affymetrix cDNA microarray chip (Pvi_cDNAa520831) containing 122 973 probe sets was designed from PviUT1.2 sequences, and used to develop a Gene Expression Atlas for switchgrass (PviGEA). The PviGEA contains quantitative transcript data for all major organ systems of switchgrass throughout development. We developed a web server that enables flexible, multifaceted analyses of PviGEA transcript data. The PviGEA was used to identify representatives of all known genes in the phenylpropanoid–monolignol biosynthesis pathway.
OsCYP2, a chaperone involved in degradation of auxin‐responsive proteins, plays crucial roles in rice lateral root initiation
Authors: Kang Bo , Zhang Zhongchen , Wang Lingling , Zheng Libin , Mao Weihua , Li Meifei , Wu Yunrong , Wu Ping , Mo Xiaorong 
Published: January 2013

SummaryAuxin plays a pivotal role in many facets of plant development. It acts by inducing the interaction between auxin‐responsive [auxin (AUX)/indole‐3‐acetic acid (IAA)] proteins and the ubiquitin protein ligase SCFTIR to promote the degradation of the AUX/IAA proteins. Other cofactors and chaperones that participate in auxin signaling remain to be identified. Here, we characterized rice (Oryza sativa) plants with mutations in a cyclophilin gene (OsCYP2). cyp2 mutants showed defects in auxin responses and exhibited a variety of auxin‐related growth defects in the root. In cyp2 mutants, lateral root initiation was blocked after nuclear migration but before the first anticlinal division of the pericycle cell. Yeast two‐hybrid and in vitro pull‐down results revealed an association between OsCYP2 and the co‐chaperone Suppressor of G2 allele of skp1 (OsSGT1). Luciferase complementation imaging assays further supported this interaction. Similar to previous findings in an Arabidopsis thaliana SGT1 mutant (atsgt1b), degradation of AUX/IAA proteins was retarded in cyp2 mutants treated with exogenous 1‐naphthylacetic acid. Our results suggest that OsCYP2 participates in auxin signal transduction by interacting with OsSGT1.
Overexpression of a soybean nuclear localized type–III DnaJ domain‐containing HSP40 reveals its roles in cell death and disease resistance
Authors: Liu Jian‐Zhong , Whitham Steven A. 
Published: January 2013

SummaryHeat‐shock proteins such as HSP70 and HSP90 are important molecular chaperones that play critical roles in biotic and abiotic stress responses; however, the involvement of their co‐chaperones in stress biology remains largely uninvestigated. In a screen for candidate genes stimulating cell death in Glycine max (soybean), we transiently overexpressed full‐length cDNAs of soybean genes that are highly induced during soybean rust infection in Nicotiana benthamiana leaves. Overexpression of a type‐III DnaJ domain‐containing HSP40 (GmHSP40.1), a co‐chaperone of HSP70, caused hypersensitive response (HR)‐like cell death. The HR‐like cell death was dependent on MAPKKKα and WIPK, because silencing each of these genes suppressed the HR. Consistent with the presence of a nuclear localization signal (NLS) motif within the GmHSP40.1 coding sequence, GFP‐GmHSP40.1 was exclusively present in nuclear bodies or speckles. Nuclear localization of GmHSP40.1 was necessary for its function, because deletion of the NLS or addition of a nuclear export signal abolished its HR‐inducing ability. GmHSP40.1 co‐localized with HcRed‐SE, a protein involved in pri‐miRNA processing, which has been shown to be co‐localized with SR33‐YFP, a protein involved in pre‐mRNA splicing, suggesting a possible role for GmHSP40.1 in mRNA splicing or miRNA processing, and a link between these processes and cell death. Silencing GmHSP40.1 enhanced the susceptibility of soybean plants to Soybean mosaic virus, confirming its positive role in pathogen defense. Together, the results demonstrate a critical role of a nuclear‐localized DnaJ domain‐containing GmHSP40.1 in cell death and disease resistance in soybean.
The rice faded green leaf locus encodes protochlorophyllide oxidoreductase B and is essential for chlorophyll synthesis under high light conditions
Authors: Sakuraba Yasuhito , Rahman Md Lutfor , Cho Sung‐Hwan , Kim Ye‐Sol , Koh Hee‐Jong , Yoo Soo‐Cheul , Paek Nam‐Chon 
Published: January 2013

SummaryNADPH:protochlorophyllide oxidoreductase (POR) catalyzes photoreduction of protochlorophyllide (Pchlide) to chlorophyllide in chlorophyll (Chl) synthesis, and is required for prolamellar body (PLB) formation in etioplasts. Rice faded green leaf (fgl) mutants develop yellow/white leaf variegation and necrotic lesions during leaf elongation in field‐grown plants. Map‐based cloning revealed that FGL encodes OsPORB, one of two rice POR isoforms. In fgl, etiolated seedlings contained smaller PLBs in etioplasts, and lower levels of total and photoactive Pchlide. Under constant or high light (HL) conditions, newly emerging green leaves rapidly turned yellow and formed lesions. Increased levels of non‐photoactive Pchlide, which acts as a photosensitizer, may cause reactive oxygen accumulation and lesion formation. OsPORA expression is repressed by light and OsPORB expression is regulated in a circadian rhythm in short‐day conditions. OsPORA was expressed at high levels in developing leaves and decreased dramatically in fully mature leaves, whereas OsPORB expression was relatively constant throughout leaf development, similar to expression patterns of AtPORA and AtPORB in Arabidopsis. However, OsPORB expression is rapidly upregulated by HL treatment, similar to the fluence rate‐dependent regulation of AtPORC. This suggests that OsPORB function is equivalent to both AtPORB and AtPORC functions. Our results demonstrate that OsPORB is essential for maintaining light‐dependent Chl synthesis throughout leaf development, especially under HL conditions, whereas OsPORA mainly functions in the early stages of leaf development. Developmentally and physiologically distinct roles of monocot OsPORs are discussed by comparing with those of dicot AtPORs.
Mechanisms responsible for beneficial and adverse effects of rosiglitazone in a rat model of acute cardiac ischaemia–reperfusion
Authors: Palee Siripong , Weerateerangkul Punate , Chinda Kroekkiat , Chattipakorn Siriporn C. , Chattipakorn Nipon 
Published: January 2013

New Findings
What is the central question of this study?Controversy exists regarding the beneficial and adverse effects of rosiglitazone. We sought to determine the effects of rosiglitazone in the heart during ischaemia–reperfusion injury.
What is the main finding and what is its importance?We demonstrated that rosiglitazone simultaneously exerted both beneficial and adverse effects on the heart during ischaemia–reperfusion. These findings provided new mechanistic insights into the effects of this drug, and elucidate the possibility of its undesirable effects in patients taking this drug.
Despite debate regarding its cardioprotective and pro‐arrhythmic effects, the precise mechanisms of action of rosiglitazone on the heart are still unclear. We determined the mechanistic effects of rosiglitazone on cardiac function, arrhythmias and infarct size during cardiac ischaemia–reperfusion. Twenty‐six rats were used. In each rat, either rosiglitazone or saline solution was administered intravenously prior to a 30 min left anterior descending coronary artery ligation and a 120 min reperfusion. Cardiac function, infarct size, myocardial levels of connexin43, Bax/Bcl‐2, cytochrome c, caspase‐3, caspase‐8, Akt, tumour necrosis factor‐α and interleukin‐4 and cardiac mitochondrial function were determined. Isolated cardiomyocytes were used for studying intracellular calcium. Rosiglitazone did not alter cardiac function during the ischaemia–reperfusion periods, but increased the arrhythmia score and mortality rate, decreased the time to onset of ventricular fibrillation and prolonged the Ca2+ decay rate, in comparison to the saline‐injected group (P < 0.05). However, the infarct size in the rosiglitazone‐injected group was reduced (P < 0.05). Rosiglitazone decreased the levels of connexin43 phosphorylation, active caspase‐8 and tumour necrosis factor‐α, but increased the level of procaspase‐3. However, levels of Bax/Bcl‐2, cytochrome c, Akt and interleukin‐4 and the cardiac mitochondrial function were not different between the two groups. Rosiglitazone simultaneously exerted both beneficial and adverse cardiac effects in the heart exposed to ischaemia–reperfusion. Although it decreased the infarct size via the extrinsic anti‐apoptotic pathway and anti‐inflammatory effects, rosiglitazone facilitated a fatal arrhythmia by decreasing connexin43 phosphorylation and prolonging the Ca2+ decay rate in ischaemia–reperfusion. The higher mortality rate in the rosiglitazone‐injected group suggests that its undesirable effect was more pronounced than its benefit on infarct size reduction.
3D image‐guided robotic needle positioning system for small animal interventions
Authors: Bax Jeffrey S. , Waring Christopher S. R. , Sherebrin Shi , Stapleton Shawn , Hudson Thomas J. , Jaffray David A. , Lacefield James C. , Fenster Aaron 
Published: January 2013

Purpose:This paper presents the design of a micro‐CT guided small animal robotic needle positioning system. In order to simplify the robotic design and maintain a small targeting error, a novel implementation of the remote center of motion is used in the system. The system has been developed with the objective of achieving a mean targeting error of <200 μm while maintaining a high degree of user friendliness.Methods:The robot is compact enough to operate within a 25 cm diameter micro‐CT bore. Small animals can be imaged and an intervention performed without the need to transport the animal from one workspace to another. Not requiring transport of the animal reduces opportunities for targets to shift from their localized position in the image and simplifies the workflow of interventions. An improved method of needle calibration is presented that better characterizes the calibration using the position of the needle tip in photographs rather than the needle axis. A calibration fixture was also introduced, which dramatically reduces the time requirements of calibration while maintaining calibration accuracy. Two registration modes have been developed to correspond the robot coordinate system with the coordinate system of the micro‐CT scanner. The two registration modes offer a balance between the time required to complete a registration and the overall registration accuracy. The development of slow high accuracy and fast low accuracy registration modes provides users with a degree of flexibility in selecting a registration mode best suited for their application.Results:The target registration error (TRE) of the higher accuracy primary registration was TREprimary = 31 ± 12 μm. The error in the lower accuracy combined registration was TREcombined = 139 ± 63 μm. Both registration modes are therefore suitable for small‐animal needle interventions. The targeting accuracy of the robotic system was characterized using targeting experiments in tissue‐mimicking gelatin phantoms. The results of the targeting experiments were combined with the known calibration and needle deflection errors to provide a more meaningful measure of the needle positioning accuracy of the system. The combined targeting errors of the system were 149 ± 41 μm and 218 ± 38 μm using the primary and combined registrations, respectively. Finally, pilot in vivo experiments were successfully completed to demonstrate the performance of the system in a biomedical application.Conclusions:The device was able to achieve the desired performance with an error of <200 μm and improved repeatability when compared to other designs. The device expands the capabilities of image‐guided interventions for preclinical biomedical applications.
Gafchromic EBT2 film dosimetry in reflection mode with a novel plan‐based calibration method
Authors: Méndez I. , Hartman V. , Hudej R. , Strojnik A. , Casar B. 
Published: January 2013

Purpose:A dosimetric system formed by Gafchromic EBT2 radiochromic film and Epson Expression 10000XL flatbed scanner was commissioned for dosimetry. In this paper, several open questions concerning the commissioning of radiochromic films for dosimetry were addressed: (a) is it possible to employ this dosimetric system in reflection mode; (b) if so, can the methods used in transmission mode also be used in reflection mode; (c) is it possible to obtain accurate absolute dose measurements with Gafchromic EBT2 films; (d) which calibration method should be followed; (e) which calibration models should be used; and (f) does three‐color channel dosimetry offer a significant improvement over single channel dosimetry. The purpose of this paper is to help clarify these questions.Methods:In this study, films were scanned in reflection mode, the effect of surrounding film was evaluated and the feasibility of EBT2 film dosimetry in reflection mode was studied. EBT2's response homogeneity has been reported to lead to excessive dose uncertainties. To overcome this problem, a new plan‐based calibration method was implemented. Plan‐based calibration can use every pixel and each of the three color channels of the scanned film to obtain the parameters of the calibration model. A model selection analysis was conducted to select lateral correction and sensitometric curve models. The commonly used calibration with fragments was compared with red‐channel plan‐based calibration and with three‐channel plan‐based calibration.Results:No effect of surrounding film was found in this study. The film response inhomogeneity in EBT2 films was found to be important not only due to differences in the fog but also due to differences in sensitivity. The best results for lateral corrections were obtained using absolute corrections independent of the dose. With respect to the sensitometric curves, an empirical polynomial fit of order 4 was found to obtain results equivalent to a gamma‐distributed single hit model based on physical assumptions. Three‐channel dosimetry was found to be substantially superior to red‐channel dosimetry.Conclusions:Reflection mode with Gafchromic EBT2 radiochromic film was found to be a viable alternative to transmission mode. The same methods that are used in transmission mode can be followed in reflection mode. A novel plan‐based method was developed for calibration and multichannel dosimetry. This novel method offers increased robustness against film response inhomogeneities and reduces considerably the time required for calibration.
A comparative study of small field total scatter factors and dose profiles using plastic scintillation detectors and other stereotactic dosimeters: The case of the CyberKnife
Authors: Morin Jonathan , Béliveau‐Nadeau Dominic , Chung Eunah , Seuntjens Jan , Thériault Dany , Archambault Louis , Beddar Sam , Beaulieu Luc 
Published: January 2013

Purpose:Small‐field dosimetry is challenging, and the main limitations of most dosimeters are insufficient spatial resolution, water nonequivalence, and energy dependence. The purpose of this study was to compare plastic scintillation detectors (PSDs) to several commercial stereotactic dosimeters by measuring total scatter factors and dose profiles on a CyberKnife system.Methods:Two PSDs were developed, having sensitive volumes of 0.196 and 0.785 mm3, and compared with other detectors. The spectral discrimination method was applied to subtract Čerenkov light from the signal. Both PSDs were compared to four commercial stereotactic dosimeters by measuring total scatter factors, namely, an IBA dosimetry stereotactic field diode (SFD), a PTW 60008 silicon diode, a PTW 60012 silicon diode, and a microLion. The measured total scatter factors were further compared with those of two independent Monte Carlo studies. For the dose profiles, two commercial detectors were used for the comparison, i.e., a PTW 60012 silicon diode and Gafchromics EBT2. Total scatter factors for a CyberKnife system were measured in circular fields with diameters from 5 to 60 mm. Dose profiles were measured for the 5‐ and 60‐mm cones. The measurements were performed in a water tank at a 1.5‐cm depth and an 80‐cm source‐axis distance.Results:The total scatter factors measured using all the detectors agreed within 1% with the Monte Carlo values for cones of 20 mm or greater in diameter. For cones of 10–20 mm in diameter, the PTW 60008 silicon diode was the only dosimeter whose measurements did not agree within 1% with the Monte Carlo values. For smaller fields (<10 mm), each dosimeter type showed different behaviors. The silicon diodes over‐responded because of their water nonequivalence; the microLion and 1.0‐mm PSD under‐responded because of a volume‐averaging effect; and the 0.5‐mm PSD was the only detector within the uncertainties of the Monte Carlo simulations for all the cones. The PSDs, the PTW 60012 silicon diode, and the Gafchromics EBT2 agreed within 2% and 0.2 mm (gamma evaluation) for the measured dose profiles except in the tail of the 60‐mm cone.Conclusions:Silicon diodes can be used to accurately measure small‐field dose profiles but not to measure total scatter factors, whereas PSDs can be used to accurately measure both. The authors' measurements show that the use of a 1.0‐mm PSD resulted in a negligible volume‐averaging effect (under‐response of ≈1%) down to a field size of 5 mm. Therefore, PSDs are strong candidates to become reference radiosurgery detectors for beam characterization and quality assurance measurements.
A system for MRI‐guided transperineal delivery of needles to the prostate for focal therapy
Authors: Cepek Jeremy , Chronik Blaine A. , Lindner Uri , Trachtenberg John , Davidson Sean R. H. , Bax Jeffrey , Fenster Aaron 
Published: January 2013

Purpose:To demonstrate the capabilities of a new magnetic resonance imaging (MRI)‐guided system for delivering needles to the prostate for focal therapy. Included is a presentation of the design of the system and its user interface, evaluation of MR‐compatibility, and quantitative evaluation of guidance accuracy and repeatability within the bore of a clinical MRI scanner.Methods:The use of MRI for visualization of tumors, intraoperative visualization of interventional tools, and thermometry for controlled ablation of lesions is becoming increasingly prevalent. In this work, the authors present a prototype system for guiding needles to prostate tumors within the bore of an MRI scanner for use in focal laser thermal ablation of prostate tumors. The system consists of a manually actuated trajectory alignment device that allows a physician to precisely align a set of needle guides with an intended target in the prostate within the bore of a clinical closed‐bore MRI scanner. Needle insertion is then performed transperineally, with the patient in the bore of the MRI, and custom software provides monitoring of thermal ablative procedures.Results:The system is shown to have a minimal effect on image distortion, and only a 6% decrease in image signal‐to‐noise ratio. Through needle insertion tests in tissue‐mimicking phantoms, the system's potential for reliably guiding needles to intra‐MR targets within 2.64 mm has been demonstrated. Use of the system to deliver focal laser ablation therapy to two patients showed that it can be used to deliver needles with minimal disruption of workflow, and in less time than when insertions are performed freehand or with a fixed grid template.Conclusions:A system for delivering needles to a patient's prostate for focal therapy within the bore of an MRI scanner has been developed. Results from needle insertion tests in phantoms suggest that the system has the potential to provide accurate delivery of focal therapy to prostate tumors of the smallest clinically significant size. Initial tests in two patients showed that needle deflection was larger than in phantoms, but methods of manually compensating for this effect were employed and needles were delivered to treatment sites with sufficient accuracy to deliver effective treatment. In addition, the treatment was delivered in less time than with a fixed grid template or freehand insertions. Despite this success, methods of reducing needle deflection are needed in order to fully utilize the potential of this system, and further reduce total procedure time.