bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genomics ofSaccharomyces cerevisiaehuman isolates: passengers, colonizers, invaders
Authors: De Filippo Carlotta , Di Paola Monica , Stefanini Irene , Rizzetto Lisa , Berná Luisa , Ramazzotti Matteo , Dapporto Leonardo , Rivero Damariz , Gut Ivo G. , Gut Marta , Bayés Mónica , Legras Jean-Luc , Viola Roberto , Massi-Benedetti Cristina , De Luca Antonella , Romani Luigina , Lionetti Paolo , Cavalieri Duccio 
Published: January 2014

AbstractThe quest for the ecological niches ofSaccharomyces cerevisiaeranged from wineries to oaks and more recently to the gut ofCrabroWasps. Here we propose the role of the human gut in shapingS. cerevisiaeevolution, presenting the genetic structure of a previously unknown population of yeasts, associated with Crohn’s disease, providing evidence for clonal expansion within human’s gut. To understand the role of immune function in the human-yeast interaction we classified strains according to their immunomodulatory properties, discovering a set of genetically homogeneous isolates, capable of inducing anti-inflammatory signalsviaregulatory T cells proliferation, and on the contrary, a positive association between strain mosaicism and ability to elicit inflammatory, IL-17 driven, immune responses. The approach integrating genomics with immune phenotyping showed selection on genes involved in sporulation and cell wall remodeling as central for the evolution ofS. cerevisiaeCrohn’s strains from passengers to commensals to potential pathogens.
ANGUSTIFOLIA3 Binds to SWI/SNF Chromatin Remodeling Complexes to Regulate Transcription during Arabidopsis Leaf Development
Authors: Vercruyssen Liesbeth , Verkest Aurine , Gonzalez Nathalie , Heyndrickx Ken S. , Eeckhout Dominique , Han Soon-Ki , Jégu Teddy , Archacki Rafal , Van Leene Jelle , Andriankaja Megan , De Bodt Stefanie , Abeel Thomas , Coppens Frederik , Dhondt Stijn , De Milde Liesbeth , Vermeersch Mattias , Maleux Katrien , Gevaert Kris , Jerzmanowski Andrzej , Benhamed Moussa , Wagner Doris , Vandepoele Klaas , De Jaeger Geert , Inzé Dirk 
Published: January 2014

Abstract
The transcriptional coactivator ANGUSTIFOLIA3 (AN3) stimulates cell proliferation during Arabidopsis thaliana leaf development, but the molecular mechanism is largely unknown. Here, we show that inducible nuclear localization of AN3 during initial leaf growth results in differential expression of important transcriptional regulators, including GROWTH REGULATING FACTORs (GRFs). Chromatin purification further revealed the presence of AN3 at the loci of GRF5, GRF6, CYTOKININ RESPONSE FACTOR2, CONSTANS-LIKE5 (COL5), HECATE1 (HEC1), and ARABIDOPSIS RESPONSE REGULATOR4 (ARR4). Tandem affinity purification of protein complexes using AN3 as bait identified plant SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complexes formed around the ATPases BRAHMA (BRM) or SPLAYED. Moreover, SWI/SNF ASSOCIATED PROTEIN 73B (SWP73B) is recruited by AN3 to the promoters of GRF5, GRF3, COL5, and ARR4, and both SWP73B and BRM occupy the HEC1 promoter. Furthermore, we show that AN3 and BRM genetically interact. The data indicate that AN3 associates with chromatin remodelers to regulate transcription. In addition, modification of SWI3C expression levels increases leaf size, underlining the importance of chromatin dynamics for growth regulation. Our results place the SWI/SNF-AN3 module as a major player at the transition from cell proliferation to cell differentiation in a developing leaf.
A Wheat SIMILAR TO RCD-ONE Gene Enhances Seedling Growth and Abiotic Stress Resistance by Modulating Redox Homeostasis and Maintaining Genomic Integrity
Authors: Liu Shuantao , Liu Shuwei , Wang Mei , Wei Tiandi , Meng Chen , Wang Meng , Xia Guangmin 
Published: January 2014

Abstract
Plant growth inhibition is a common response to salinity. Under saline conditions, Shanrong No. 3 (SR3), a bread wheat (Triticum aestivum) introgression line, performs better than its parent wheat variety Jinan 177 (JN177) with respect to both seedling growth and abiotic stress tolerance. Furthermore, the endogenous reactive oxygen species (ROS) was also elevated in SR3 relative to JN177. The SR3 allele of sro1, a gene encoding a poly(ADP ribose) polymerase (PARP) domain protein, was identified to be crucial for both aspects of its superior performance. Unlike RADICAL-INDUCED CELL DEATH1 and other Arabidopsis thaliana SIMILAR TO RCD-ONE (SRO) proteins, sro1 has PARP activity. Both the overexpression of Ta-sro1 in wheat and its heterologous expression in Arabidopsis promote the accumulation of ROS, mainly by enhancing the activity of NADPH oxidase and the expression of NAD(P)H dehydrogenase, in conjunction with the suppression of alternative oxidase expression. Moreover, it promotes the activity of ascorbate-GSH cycle enzymes and GSH peroxidase cycle enzymes, which regulate ROS content and cellular redox homeostasis. sro1 is also found to be involved in the maintenance of genomic integrity. We show here that the wheat SRO has PARP activity; such activity could be manipulated to improve the growth of seedlings exposed to salinity stress by modulating redox homeostasis and maintaining genomic stability.
DNA Replicons for Plant Genome Engineering
Authors: Baltes Nicholas J. , Gil-Humanes Javier , Cermak Tomas , Atkins Paul A. , Voytas Daniel F. 
Published: January 2014

AbstractSequence-specific nucleases enable facile editing of higher eukaryotic genomic DNA; however, targeted modification of plant genomes remains challenging due to ineffective methods for delivering reagents for genome engineering to plant cells. Here, we use geminivirus-based replicons for transient expression of sequence-specific nucleases (zinc-finger nucleases, transcription activator–like effector nucleases, and the clustered, regularly interspaced, short palindromic repeat/Cas system) and delivery of DNA repair templates. In tobacco (Nicotiana tabacum), replicons based on the bean yellow dwarf virus enhanced gene targeting frequencies one to two orders of magnitude over conventional Agrobacterium tumefaciens T-DNA. In addition to the nuclease-mediated DNA double-strand breaks, gene targeting was promoted by replication of the repair template and pleiotropic activity of the geminivirus replication initiator proteins. We demonstrate the feasibility of using geminivirus replicons to generate plants with a desired DNA sequence modification. By adopting a general plant transformation method, plantlets with a desired DNA change were regenerated in &lt;6 weeks. These results, in addition to the large host range of geminiviruses, advocate the use of replicons for plant genome engineering.
Cardiolipin-Mediated Mitochondrial Dynamics and Stress Response inArabidopsis
Authors: Pan Ronghui , Jones A. Daniel , Hu Jianping 
Published: January 2014

AbstractMitochondria are essential and dynamic organelles in eukaryotes. Cardiolipin (CL) is a key phospholipid in mitochondrial membranes, playing important roles in maintaining the functional integrity and dynamics of mitochondria in animals and yeasts. However, CL's role in plants is just beginning to be elucidated. In this study, we used Arabidopsis thaliana to examine the subcellular distribution of CL and CARDIOLIPIN SYNTHASE (CLS) and analyzed loss-of-function cls mutants for defects in mitochondrial morphogenesis and stress response. We show that CL localizes to mitochondria and is enriched at specific domains, and CLS targets to the inner membrane of mitochondria with its C terminus in the intermembrane space. Furthermore, cls mutants exhibit significantly impaired growth as well as altered structural integrity and morphogenesis of mitochondria. In contrast to animals and yeasts, in which CL's effect on mitochondrial fusion is more profound, Arabidopsis CL plays a dominant role in mitochondrial fission and exerts this function, at least in part, through stabilizing the protein complex of the major mitochondrial fission factor, DYNAMIN-RELATED PROTEIN3. CL also plays a role in plant responses to heat and extended darkness, stresses that induce programmed cell death. Our study has uncovered conserved and plant-specific aspects of CL biology in mitochondrial dynamics and the organism response to environmental stresses.
Expression, purification, crystallization and preliminary X-ray analysis of the PaaI-like thioesterase SAV0944 from Staphylococcus aureus
Authors: Khandokar Yogesh B. , Roman Noelia , Smith Kate M. , Srivastava Parul , Forwood Jade K. 
Published: January 2014

Staphylococcus aureus is the causative agent of many diseases, including meningitis, bacteraemia, pneumonia, food poisoning and toxic shock syndrome. Structural characterization of the PaaI-like thioesterase SAV0944 (SaPaaI) from S. aureus subsp. aureus Mu50 will aid in understanding its potential as a new therapeutic target by knowledge of its molecular details and cellular functions. Here, the recombinant expression, purification and crystallization of SaPaaI thioesterase from S. aureus are reported. This protein initially crystallized with the ligand coenzyme A using the hanging-drop vapour-diffusion technique with condition No. 40 of Crystal Screen from Hampton Research at 296 K. Optimal final conditions consisting of 24% PEG 4000, 100 mM sodium citrate pH 6.5, 12% 2-propanol gave single diffraction-quality crystals. These crystals diffracted to beyond 2 Å resolution at the Australian Synchrotron and belonged to space group P1211, with unit-cell parameters a = 44.05, b = 89.05, c = 60.74 Å, β = 100.5°. Initial structure determination and refinement gave an R factor and R
free of 17.3 and 22.0%, respectively, confirming a positive solution in obtaining phases using molecular replacement.
Competitive effects of co‐operation with suppliers and buyers in the sawmill industry
Authors: Gueimonde‐Canto Ana , González‐Benito Javier , Manuel García‐Vázquez José 
Published: January 2014

PurposeThe present paper proposes simultaneous research into the effects of co‐operation with buyers and suppliers on company performance, and how both types of co‐operation interact in one specific industry.Design/methodology/approachThe paper conducts an analysis of a sample of 80 sawmills in the Spanish regions of Galicia and the Basque Country, comprising most of the wood production in Spain.FindingsContrary to prior research, the results suggest that contextual factors, inherent to each supply chain, affect the relationship between supplier‐customer co‐operation and performance.Research limitations/implicationsThe findings lead one to argue that some traditional arguments in favour of co‐operation with buyers and suppliers might not be applicable to specific industries, positions in the value chain or exchanged products, and that industry‐specific variables should be included in future research.Practical implicationsSawmills appear to benefit only from co‐operation with buyers, but not from co‐operation with suppliers. Furthermore, the two types of co‐operation do not appear to generate synergy.Originality/valueThe study adopts a systemic view of the supply chain and argues that industry‐specific factors, and position in the value chain, should be included as control variables in empirical work researching the competitive consequences of co‐operation in the value chain.
Harlequin color change in two preterm newborns
Authors: Dang Dan , Zhou Wenli , Liu Ying , Wu Hui 
Published: January 2014

AbstractHarlequin color change is a benign transient skin change usually seen in the neonatal period with unknown etiology. It has been rarely reported in preterm infants. Herein, we report two cases of harlequin color change developed in premature infants without any adverse consequences. During the event, one infant was receiving antibiotic treatment for an Escherichia coli bacteremia in addition to routine supportive care and the other one was in a very stable condition. Both preterm infants were also diagnosed to have a patent ductus arteriosus. As a benign transient skin change, harlequin color change should be recognized properly to avoid unnecessary treatment.
Mycosis fungoides palmaris et plantaris successfully treated with radiotherapy: Case report and mini‐review of the published work
Authors: Nakai Noriaki , Hagura Asami , Yamazato Shiho , Katoh Norito 
Published: January 2014

AbstractMycosis fungoides palmaris et plantaris (MFPP) is a rare variant of cutaneous T‐cell lymphoma limited to the palms and soles that is not widely recognized because of its uncommon occurrence. We report a 73‐year‐old Japanese man who presented with an erosion on the left dorsal hand, a reddish tumor on the right palm, and hyperkeratotic erythematous plaques on the right sole. Skin biopsy showed histological features of mycosis fungoides (MF) with invasion into the deeper layers of skin. There was no visceral or lymph node invasion. We diagnosed this case as MFPP. External beam radiotherapy (EBRT) was performed to treat the hand lesions. Combination treatment with topical steroids and topical psoralen plus ultraviolet light therapy was performed to treat the right sole lesion, but was ineffective. Therefore, sequential EBRT was performed. Complete remission of all lesions was obtained. This is the first report of MFPP with a locally advanced tumor for which the efficacy of radiotherapy is described in detail. MFPP lesions occur on the dorsal aspect of hand or foot, and here we propose a classification of MFPP as hand and foot MF. The pathogenesis of MFPP is still unclear and further accumulation of data is required.
Epstein–Barr virus‐associated T/natural killer‐cell lymphoproliferative disorders
Authors: Park Sanghui , Ko Young H. 
Published: January 2014

AbstractPrimary infection with Epstein–Barr virus (EBV) is usually asymptomatic and, in a normal host, EBV remains latent in B cells after primary infection for the remainder of life. Uncommonly, EBV can infect T or natural killer (NK) cells in a person with a defect in innate immunity, and EBV infection can cause unique systemic lymphoproliferative diseases (LPD) of childhood. Primary infection in young children can be complicated by hemophagocytic lymphohistiocytosis or fulminant systemic T‐cell LPD of childhood. Uncommonly, patients can develop chronic active EBV (CAEBV) disease‐type T/NK LPD, which includes CAEBV infection of the systemic form, hydroa vacciniforme‐like T‐cell LPD, and mosquito‐bite hypersensitivity. The clinical course of CAEBV disease‐type T/NK LPD can be smoldering, persistent or progressive, depending on the balance between viral factors and host immunity. Aggressive NK‐cell leukemia, hydroa vacciniforme‐like T‐cell lymphoma, or uncommonly extranodal NK/T‐cell lymphoma can develop in children and young adults with CAEBV disease‐type T/NK‐cell LPD. Extranodal T/NK‐cell lymphoma is a disease of adults, and its incidence begins to increase in the third decade and comprises the major subtype of T/NK LPD throughout life. Aggressive NK‐cell leukemia and nodal T/NK‐cell lymphoma of the elderly are fulminant diseases, and immune senescence may be an important pathogenetic factor. This review describes the current progress in identifying different types of EBV‐associated T/NK‐cell LPD and includes a brief presentation of data from Korea.
Skin manifestations of adult T‐cell leukemia/lymphoma: Clinical, cytological and immunological features
Authors: Tokura Yoshiki , Sawada Yu , Shimauchi Takatoshi 
Published: January 2014

AbstractAdult T‐cell leukemia/lymphoma (ATLL) is a malignancy of mature T cells caused by human T‐cell leukemia virus type I. The endemic areas include Japan, especially in Kyushu, the Caribbean, Papua New Guinea, South America and Africa. Approximately 50% of ATLL patients exhibit skin manifestations. Cytologically, ATLL tumor cells are characterized by CD4+CD25+ regulatory T‐cell phenotype, high expressions of CCR4, and programmed cell death (PD)‐1 and PD‐ligand 1. The skin eruptions are categorized into six types: patch, plaque, multipapular, nodulotumoral, erythrodermic and purpuric. The overall survival of the eruption‐bearing patients was poorer than that of the non‐eruption‐bearing patients in acute, chronic and smoldering types, but the survival levels of both groups were comparable in lymphoma type. The prognosis was poor in the order of: erythrodermic, nodulotumoral, multipapular/purpuric, plaque, then patch. Multivariate analysis revealed that the eruption type is an independent prognostic factor for ATLL. Patients may have other skin manifestations, secondary and infective lesions.
Current therapy of choice for cutaneous lymphomas: Complementary to the Japanese Dermatological Association/Japanese Skin Cancer Society guidelines
Authors: Iwatsuki Keiji , Hamada Toshihisa ,   Japanese Skin Cancer Society – Lymphoma Study Group
Published: January 2014

AbstractThe first Japanese edition of guidelines for management of cutaneous lymphoma was published jointly in 2009 by the Japanese Dermatological Association (JDA) and the Japanese Skin Cancer Society (JSCS) – Lymphoma Study Group; the guidelines were revised in 2011, and published in English in 2013. The JDA/JSCS guidelines are unique because they describe information and management practices for lymphomas specific to Asia, such as adult T‐cell leukemia/lymphoma and extranodal natural killer/T‐cell lymphoma, nasal type. In the present article, we have highlighted the essential points of management for cutaneous lymphomas in Asia. In order to complement the guidelines, we have added further information and our clinical experience of some currently available agents for cutaneous lymphomas in Japan.
Antiviral activity of extracts from Morinda citrifolia leaves and chlorophyll catabolites, pheophorbide a and pyropheophorbide a, against hepatitis C virus
Authors: Ratnoglik Suratno Lulut , Aoki Chie , Sudarmono Pratiwi , Komoto Mari , Deng Lin , Shoji Ikuo , Fuchino Hiroyuki , Kawahara Nobuo , Hotta Hak 
Published: January 2014

AbstractThe development of complementary and/or alternative drugs for treatment of hepatitis C virus (HCV) infection is still needed. Antiviral compounds in medicinal plants are potentially good targets to study. Morinda citrifolia is a common plant distributed widely in Indo‐Pacific region; its fruits and leaves are food sources and are also used as a treatment in traditional medicine. In this study, using a HCV cell culture system, it was demonstrated that a methanol extract, its n‐hexane, and ethyl acetate fractions from M. citrifolia leaves possess anti‐HCV activities with 50%‐inhibitory concentrations (IC50) of 20.6, 6.1, and 6.6 μg/mL, respectively. Bioactivity‐guided purification and structural analysis led to isolation and identification of pheophorbide a, the major catabolite of chlorophyll a, as an anti‐HCV compound present in the extracts (IC50  = 0.3 μg/mL). It was also found that pyropheophorbide a possesses anti‐HCV activity (IC50 = 0.2 μg/mL). The 50%‐cytotoxic concentrations (CC50) of pheophorbide a and pyropheophorbide a were 10.0 and 7.2 μg/mL, respectively, their selectivity indexes being 33 and 36, respectively. On the other hand, chlorophyll a, sodium copper chlorophyllin, and pheophytin a barely, or only marginally, exhibited anti‐HCV activities. Time‐of‐addition analysis revealed that pheophorbide a and pyropheophorbide a act at both entry and the post‐entry steps. The present results suggest that pheophorbide a and its related compounds would be good candidates for seed compounds for developing antivirals against HCV.
Pneumocystis jirovecii colonization is associated with enhanced Th1 inflammatory gene expression in lungs of humans with chronic obstructive pulmonary disease
Authors: Fitzpatrick Meghan E. , Tedrow John R. , Hillenbrand Maria E. , Lucht Lorrie , Richards Thomas , Norris Karen A. , Zhang Yingze , Sciurba Frank C. , Kaminski Naftali , Morris Alison 
Published: January 2014

AbstractChronic obstructive pulmonary disease (COPD) is a complex disease, the pathogenesis of which remains incompletely understood. Colonization with Pneumocystis jirovecii may play a role in COPD pathogenesis; however, the mechanisms by which such colonization contributes to COPD are unknown. The objective of this study was to determine lung gene expression profiles associated with Pneumocystis colonization in patients with COPD to identify potential key pathways involved in disease pathogenesis. Using COPD lung tissue samples made available through the Lung Tissue Research Consortium (LTRC), Pneumocystis colonization status was determined by nested PCR. Microarray gene expression profiles were performed for each sample and the profiles of colonized and non‐colonized samples compared. Overall, 18 participants (8.5%) were Pneumocystis‐colonized. Pneumocystis colonization was associated with fold increase in expression of four closely related genes: INF‐γ and the three chemokine ligands CXCL9, CXCL10, and CXCL11. These ligands are chemoattractants for the common cognate receptor CXCR3, which is predominantly expressed on activated Th1 T‐lymphocytes. Although these ligand–receptor pairs have previously been implicated in COPD pathogenesis, few initiators of ligand expression and subsequent lymphocyte trafficking have been identified: our findings implicate Pneumocystis as a potential trigger. The finding of upregulation of these inflammatory genes in the setting of Pneumocystis colonization sheds light on infectious‐immune relationships in COPD.
Characterization of the Lipid Fraction of Wild Sea Urchin from the Sardinian Sea (Western Mediterranean)
Authors: Angioni Alberto , Addis Pierantonio 
Published: January 2014

AbstractThe fatty acid (FA) composition ofSpatangus purpureus, Echinus melo, Sphaerechinus granularis, andParacentrotus lividus, sea urchins, has been studied. Sea urchins were collected at different depth along Sardinia coast in the Mediterranean sea, and their gonad was measured, separated, and analyzed for FA composition by gas chromatography‐mass spectrometry. A total of 53 FAs were detected, 16 saturated (SFA), 10 monounsaturated (MUFA), 9 polyunsaturated (PUFA), and 13 highly unsaturated (HUFA). Moreover, 5 furan FAs (FFAs) were revealed for the first time in sea urchin. The HUFA and PUFA classes were the most represented accounting for almost 80% of total FAs. Among these compounds, C20:4n6 (19.64, 20.52, 23.37, and 8.48 mg/g, respectively) and C22:6n3 (19.68, 20.05, 3.83, and 1.78 mg/g, respectively) were the most abundant. The results of principal component analysis indicated that the sea urchin samples could be clearly discriminated with respect to their FAs composition.
Characteristics of Miniature Cheddar‐Type Cheese Made by Microbial Rennet from Bacillus amyloliquefaciens: A Comparison with Commercial Calf Rennet
Authors: An Zhigang , He Xiaoling , Gao Weidong , Zhao Wei , Zhang Weibing 
Published: January 2014

AbstractMiniature Cheddar‐type cheeses were produced using microbial rennet from Bacillus amyloliquefaciens (milk‐clotting enzyme [MCE]) or calf rennet (CAR). With the exception of pH, there were no significant differences in gross composition between MCE‐cheese (MCE‐C) and CAR‐cheese (CAR‐C). The pH value of CAR‐C was significantly higher than that of MCE‐C at 40 and 60 d of ripening. The total nitrogen content of the pH 4.6‐soluble fraction obtained from MCE‐C was higher than that obtained from CAR‐C. However, nitrogen content of the 12% TCA‐soluble fraction was similar between CAR‐C and MCE‐C. The extent of αs1‐casein and β‐casein hydrolysis, measured by urea‐PAGE, was similar in both cheese samples. The hydrolysis of β‐casein was lower than that of αs1‐casein. Different reverse phase‐high‐performance liquid chromatography peptide profiles of ethanol‐soluble and ethanol‐insoluble fractions were obtained from CAR‐C and MCE‐C. The peptide content in the 2 cheese samples increased throughout ripening; the ratio of hydrophobic to hydrophilic peptides was lower in MCE‐C than in CAR‐C. Compared with CAR‐C, MCE‐C was softer as a result of higher protein hydrolysis. Microbial rennet from B. amyloliquefaciens contributed to higher proteolytic rates, which reduced ripening time.