bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silencing Nicotiana attenuata Calcium-Dependent Protein Kinases, CDPK4 and CDPK5, Strongly Up-Regulates Wound- and Herbivory-Induced Jasmonic Acid Accumulations
Authors: Yang Da-Hai , Hettenhausen Christian , Baldwin Ian T. , Wu Jianqiang 
Published: June 2012

Abstract
The plant hormone jasmonic acid (JA) plays a pivotal role in plant-insect interactions. Herbivore attack usually elicits dramatic increases in JA concentrations, which in turn activate the accumulation of metabolites that function as defenses against herbivores. Although almost all enzymes involved in the biosynthesis pathway of JA have been identified and characterized, the mechanism by which plants regulate JA biosynthesis remains unclear. Calcium-dependent protein kinases (CDPKs) are plant-specific proteins that sense changes in [Ca2+] to activate downstream responses. We created transgenic Nicotiana attenuata plants, in which two CDPKs, NaCDPK4 and NaCDPK5, were simultaneously silenced (IRcdpk4/5 plants). IRcdpk4/5 plants were stunted and aborted most of their flower primordia. Importantly, after wounding or simulated herbivory, IRcdpk4/5 plants accumulated exceptionally high JA levels. When NaCDPK4 and NaCDPK5 were silenced individually, neither stunted growth nor high JA levels were observed, suggesting that NaCDPK4 and NaCDPK5 have redundant roles. Attack from Manduca sexta larvae on IRcdpk4/5 plants induced high levels of defense metabolites that slowed M. sexta growth. We found that NaCDPK4 and NaCDPK5 affect plant resistance against insects in a JA- and JA-signaling-dependent manner. Furthermore, IRcdpk4/5 plants showed overactivation of salicylic-acid-induced protein kinase, a mitogen-activated protein kinase involved in various stress responses, and genetic analysis indicated that the increased salicylic-acid-induced protein kinase activity in IRcdpk4/5 plants was a consequence of the exceptionally high JA levels and was dependent on CORONATINE INSENSITIVE1. This work reveals the critical roles of CDPKs in modulating JA homeostasis and highlights the complex duet between JA and mitogen-activated protein kinase signaling.
SEMI-ROLLED LEAF1 Encodes a Putative Glycosylphosphatidylinositol-Anchored Protein and Modulates Rice Leaf Rolling by Regulating the Formation of Bulliform Cells
Authors: Xiang Jing-Jing , Zhang Guang-Heng , Qian Qian , Xue Hong-Wei 
Published: June 2012

Abstract
Leaf rolling is an important agronomic trait in rice (Oryza sativa) breeding and moderate leaf rolling maintains the erectness of leaves and minimizes shadowing between leaves, leading to improved photosynthetic efficiency and grain yields. Although a few rolled-leaf mutants have been identified and some genes controlling leaf rolling have been isolated, the molecular mechanisms of leaf rolling still need to be elucidated. Here we report the isolation and characterization of SEMI-ROLLED LEAF1 (SRL1), a gene involved in the regulation of leaf rolling. Mutants srl1-1 (point mutation) and srl1-2 (transferred DNA insertion) exhibit adaxially rolled leaves due to the increased numbers of bulliform cells at the adaxial cell layers, which could be rescued by complementary expression of SRL1. SRL1 is expressed in various tissues and is expressed at low levels in bulliform cells. SRL1 protein is located at the plasma membrane and predicted to be a putative glycosylphosphatidylinositol-anchored protein. Moreover, analysis of the gene expression profile of cells that will become epidermal cells in wild type but probably bulliform cells in srl1-1 by laser-captured microdissection revealed that the expression of genes encoding vacuolar H+-ATPase (subunits A, B, C, and D) and H+-pyrophosphatase, which are increased during the formation of bulliform cells, were up-regulated in srl1-1. These results provide the transcript profile of rice leaf cells that will become bulliform cells and demonstrate that SRL1 regulates leaf rolling through inhibiting the formation of bulliform cells by negatively regulating the expression of genes encoding vacuolar H+-ATPase subunits and H+-pyrophosphatase, which will help to understand the mechanism regulating leaf rolling.
The CopRS Two-Component System Is Responsible for Resistance to Copper in the Cyanobacterium Synechocystis sp. PCC 6803
Authors: Giner-Lamia Joaquín , López-Maury Luis , Reyes José C. , Florencio Francisco J. 
Published: June 2012

Abstract
Photosynthetic organisms need copper for cytochrome oxidase and for plastocyanin in the fundamental processes of respiration and photosynthesis. However, excess of free copper is detrimental inside the cells and therefore organisms have developed homeostatic mechanisms to tightly regulate its acquisition, sequestration, and efflux. Herein we show that the CopRS two-component system (also known as Hik31-Rre34) is essential for copper resistance in Synechocystis sp. PCC 6803. It regulates expression of a putative heavy-metal efflux-resistance nodulation and division type copper efflux system (encoded by copBAC) as well as its own expression (in the copMRS operon) in response to the presence of copper in the media. Mutants in this two-component system or the efflux system render cells more sensitive to the presence of copper in the media and accumulate more intracellular copper than the wild type. Furthermore, CopS periplasmic domain is able to bind copper, suggesting that CopS could be able to detect copper directly. Both operons (copMRS and copBAC) are also induced by the photosynthetic inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone but this induction requires the presence of copper in the media. The reduced response of two mutant strains to copper, one lacking plastocyanin and a second one impaired in copper transport to the thylakoid, due to the absence of the PI-type ATPases PacS and CtaA, suggests that CopS can detect intracellular copper. In addition, a tagged version of CopS with a triple HA epitope localizes to both the plasma and the thylakoid membranes, suggesting that CopS could be involved in copper detection in both the periplasm and the thylakoid lumen.
Tectono‐sedimentary evolution of the western Corinth rift (Central Greece)
Authors: Ford Mary , Rohais Sebastian , Williams Edward A. , Bourlange Sylvain , Jousselin David , Backert Nicolas , Malartre Fabrice 
Published: June 2012

AbstractThe Corinth rift (Greece) is one of the world's most active rifts. The early Plio‐Pleistocene rift is preserved in the northern Peloponnese peninsula, south of the active Corinth rift. Although chronostratigraphic resolution is limited, new structural, stratigraphic and sedimentological data for an area >400 km2 record early rift evolution in three phases separated by distinct episodes of extension rate acceleration and northward fault migration associated with major erosion. Minimum total N–S extension is estimated at 6.4–7.7 km. The earliest asymmetrical, broad rift accommodated slow extension (0.6–1 mm a−1) over >3 Myrs and closed to the west. North‐dipping faults with throws of 1000–2200 m defined narrow blocks (4–7 km) with little footwall relief. A N‐NE flowing antecedent river system infilled significant inherited relief (Lower group). In the earliest Pleistocene, significant fluvial incision coincided with a 15 km northward rift margin migration. Extension rates increased to 2–2.5 mm a−1. The antecedent rivers then built giant Gilbert‐type fan deltas (Middle group) north into a deepening lacustrine/marine basin. N‐dipping, basin margin faults accommodated throws <1500 m. Delta architecture records initiation, growth and death of this fault system over ca. 800 ka. In the Middle Pleistocene, the rift margin again migrated 5 km north. Extension rate increased to 3.4–4.8 mm a−1. This transition may correspond to an unconformity in offshore lithostratigraphy. Middle group deltas were uplifted and incised as new hangingwall deltas built into the Gulf (Upper group). A final increase to present‐day extension rates (11–16 mm a−1) probably occurred in the Holocene. Fault and fault block dimensions did not change significantly with time suggesting control by crustal rheological layering. Extension rate acceleration may be due to strain softening or to regional tectonic factors.
Down‐regulation of the microRNA processing enzyme Dicer is a prognostic factor in human colorectal cancer
Authors: Faggad Areeg , Kasajima Atsuko , Weichert Wilko , Stenzinger Albrecht , Elwali Nasr Eldin , Dietel Manfred , Denkert Carsten 
Published: June 2012

Faggad A, Kasajima A, Weichert W, Stenzinger A, Elwali N E, Dietel M & Denkert C  (2012) Histopathology 61, 552–561Down‐regulation of the microRNA processing enzyme Dicer is a prognostic factor in human colorectal cancerAims:  MicroRNA deregulation is a key feature of cancer; however, the molecular mechanisms underlying deregulation are unknown. Dicer is a central enzyme in microRNA processing essential for production of mature microRNAs which, in turn, regulate gene expression post‐transcription. The aim was to investigate whether Dicer expression in colorectal cancer correlates with conventional clinicopathological parameters and patient survival.Methods and results:  Immunohistochemical staining for Dicer was performed on tissue microarrays of 331 samples from patients with primary colorectal carcinoma. A subset (19.6%) of colorectal carcinomas was negative for Dicer. Dicer protein expression was associated significantly and inversely with disease (WHO) stage (P = 0.029), tumour grade (P = 0.001), tumour stage (P = 0.022) and nodal metastasis (P = 0.004). Negative expression of Dicer correlated significantly with shortened overall survival (P = 0.007) and was independent of other prognostic factors in multivariate analysis (Cox regression: P = 0.035, hazard ratio=1.6; 95% confidence interval 1.034–2.513). Additionally, in univariate analysis, an association of Dicer expression with survival was observed in subsets of patients without metastasis (P = 0.026), older patients (P = 0.005) and patients with advanced tumour stage (P = 0.022).Conclusion:  Dicer deregulation is linked significantly to adverse disease state and decreased overall survival in colorectal cancer. Our data suggest that reduced Dicer expression might contribute to tumour progression in colorectal cancer.
Peripheral T cell and natural killer (NK) T cell lymphomas: a clinicopathological study from a single Australian centre
Authors: McKelvie Penelope A , Thompson Philip A , Tam Constantine S 
Published: June 2012

McKelvie P A, Thompson P A & Tam C S  (2012) Histopathology 61, 212–233Peripheral T cell and natural killer (NK) T cell lymphomas: a clinicopathological study from a single Australian centreAims:  Using pathological and clinical review, to identify all cases diagnosed as peripheral T cell and natural killer (NK) T cell lymphoma over 10 years from one metropolitan Australian hospital.Methods and results:  Subtyping was performed using World Health Organization (WHO) 2008 criteria and a comprehensive immunohistochemical panel. Clinical data including follow‐up were obtained. There were 47 cases, including 11 peripheral T cell lymphomas, not otherwise specified (NOS), nine extranodal NK T cell lymphomas, nasal type (eight nasal), eight primary cutaneous anaplastic large cell lymphomas, seven angioimmunoblastic T cell lymphomas, three anaplastic lymphoma kinase (ALK)‐positive anaplastic large cell lymphomas, four ALK‐negative anaplastic large cell lymphomas, three enteropathic T cell lymphomas and two subcutaneous panniculitis‐like T cell lymphomas. Follow‐up of 46 of 47 cases (median time 45 months) revealed that 50% (23 of 46) of patients died. Five‐year survival rates were: peripheral T cell lymphoma, NOS 39%; angioimmunoblastic T cell, 43%; nasal NK T 67%; ALK‐negative anaplastic large cell lymphoma 67% (at 2 years); ALK+ anaplastic large cell lymphoma 33%; subcutaneous panniculitis‐like T cell lymphomas 100%; primary cutaneous anaplastic large cell lymphoma 86%; and enteropathic T cell lymphoma 33% (at 1 year). One patient with Lennert lymphoma suffered four late cutaneous relapses.Conclusions:  This first Australian clinicopathological series of peripheral T cell and NK T cell lymphoma shows epidemiological and survival data similar to those for Europe and North America.
Effects of ozone and chlorine postharvest treatments on quality of fresh‐cut red bell peppers
Authors: Horvitz Sandra , Cantalejo María J. 
Published: June 2012

SummaryThe effects of chlorine (200 μL L−1), ozonated water (1 μL L−1) and gaseous ozone (0.7 μL L−1) on physicochemical attributes and microbial quality of minimally processed red bell peppers were studied. In all the experiments, O2 continuously decreased and CO2 concentration increased, the pH augmented and a significant softening was observed in all the fruits. By day 14, L* values decreased in all the fruits, with the greatest changes found in the chlorinated samples (approximately 12 units). Peppers treated with the aqueous solutions showed greater changes in the quality attributes with increasing washing times and especially when chlorine was used. The exposure for three min to gaseous O3 reduced the mesophiles, psychrotrophes and fungal populations of the fresh‐cut peppers in 2.5, 3.3 and 1.8 log units, respectively. Combined with modified atmosphere, this could be an appropriate method to maintain the quality and extend the storage period of minimally processed red bell peppers.
In vitro bioaccessibility of coenzyme Q10 in enriched yoghurts
Authors: Ercan Pınar , El Sedef Nehir 
Published: June 2012

SummaryIn this study, the aim was to determine the bioaccessibilities of coenzyme Q10 (CoQ10) in yoghurt samples produced using enriched skim milk with different coenzyme Q10 preparations. First, emulsified coenzyme Q10, γ‐cyclodextrin/coenzyme Q10 complex and nanoparticle coenzyme Q10 were prepared with the reference coenzyme Q10 standard. These coenzyme Q10 preparations were added into the milk to produce coenzyme Q10 enriched yoghurt samples. Nanoparticle coenzyme Q10 was obtained as in spherical shape with 176.00 ± 50.62 nm diameter. Coenzyme Q10 bioaccessibility was found as 50.59 ± 1.88% in control yoghurt. The yoghurt enriched nanoparticle coenzyme Q10 had the highest coenzyme Q10 bioaccessibility (73.81 ± 1.61%) among the produced yoghurts (P < 0.01). Coenzyme Q10 bioaccessibilities were also found as 63.75 ± 0.91% and 46.83 ± 1.27% in yoghurts enriched with emulsified coenzyme Q10, and γ‐cyclodextrin/coenzyme Q10 complex, respectively.
Physicochemical properties of acetylated starches from some Indian kidney bean (Phaseolus vulgaris L.) cultivars
Authors: Wani Idrees A. , Sogi Dalbir S. , Gill Balmeet S. 
Published: June 2012

SummaryStarches separated from four kidney bean cultivars were modified by acetylation to reduce retrogradation and increase gel stability and compared with respective native starches (data of native starch reported by Wani et al., 2010). Acetylation was carried out by treating starches with 0.04 and 0.08 g of acetic anhydride per gram of starch dry weight basis (dwb) at 25 °C and pH between 8.0 and 8.5. The extent of acetylation increased proportionally with the concentration of acetic anhydride used. The pasting curves of 10.7% starch determined by Rapid Visco Analyzer at 160 rpm showed that acetylation decreased the setback viscosity values by 0.64–34.58% and pasting temperature by 4.4–9.2 °C when compared with the native starch. Differential scanning calorimetry observations also revealed significant (P ≤ 0.05) decrease in gelatinisation temperature of acetylated starches than the corresponding native starches. Hardness of starch gels varied between 14.3 and 44.0 g, which was significantly (P ≤ 0.05) lower than the corresponding native starch gels.
Prevalence of frailty‐related risk factors in older adults seen by community nurses
Authors: Ballard Julianne , Mooney Mary , Dempsey Orla 
Published: June 2012

ballard j., mooney m. & dempsey o. (2013) Prevalence of frailty‐related risk factors in older adults seen by community nurses. Journal of Advanced Nursing69(3), 675–684. doi: 10.1111/j.1365‐2648.2012.06054.xAbstractAims.  To describe the frequency of four frailty‐related risk factors in a cohort of older adults visited by community nurses in Dublin, Ireland.Background.  The Irish public health nursing service allows for both professional and self referral. Risk factors examined were suspected cognitive impairment, nutritional and fall risk, and activities of daily living dependence.Design.  Retrospective cross‐sectional clinical audit.Methods.  The study incorporated a retrospective clinical audit of files (N = 120) obtained from community nursing visits over 9 months in 2009–2010. A chi‐square analysis tested for association between each risk factor and oldest age, living alone, professional referral to the nursing service, and presence of formal home support.Results.  Findings revealed a cohort prevalence of suspected cognitive impairment at 16·4%. Risk of malnutrition and risk of a fall were 20·2% and 30·8%, respectively. The cohort was dependent in activities of daily living at a rate of 23·5%. Participants dependent in activities of daily living were less likely to live alone and were more likely to have referred themselves to community nursing. Associations between the four frailty‐related risk factors and receiving formal home support were not significant.Conclusion.  This study results suggest that dependency in activities of daily living (an outcome of frailty) is strongly associated with a decreased likelihood of living alone and increased likelihood of referring oneself to community nursing services. Further research is necessary to examine how frailty screening in the referral process may enhance identification of older adults’ community nursing needs in Dublin, Ireland.
The mid‐Holocene vegetation of the Mediterranean region and southern Europe, and comparison with the present day
Authors: Collins Pamela M. , Davis Basil A. S. , Kaplan Jed O. 
Published: June 2012

AbstractAim  To contribute to the intense debate surrounding the relative influence of climate and humans on Mediterranean‐region land cover over the past 6000 years, we assess the Holocene biogeography and vegetation history of southern Europe by means of an extensive pollen record dataset.Location  The Mediterranean biogeographical zone and neighbouring parts of Iberia, the Alps and Anatolia, between 30° N, 48° N, 10° W and 45° E.Methods  We compiled a southern European pollen record dataset using available pollen databases (124 sites) and other sources (74 sites), with improved spatial coverage and dating control compared with earlier studies. We used only those sites that had pollen data for both 0 ka and 6 ka. We reconstructed mid‐Holocene and present‐day biomes, arboreal pollen percentages and distribution and relative abundance of 11 key woody taxa, with anomaly maps.Results  Northern temperate forest biomes extended further south at the mid‐Holocene than at present, but not as far as earlier studies suggested. Sclerophyllous vegetation occurred along the Mediterranean coast throughout the region at 6 ka. Arboreal pollen percentages were up to 50% higher than at present. At 6 ka, Olea, Fagus and Juniperus had smaller distributions and/or abundances; Abies, Cedrus and both deciduous and evergreen Quercus had larger distributions and/or abundances; Phillyrea, Pistacia and Cistus showed minimal difference; and Pinus showed a cosmopolitan distribution with variable abundance.Main conclusions  Temporal difference analysis is more meaningful when only sites containing samples for all time slices are analysed. During the mid‐Holocene, southern Europe was more heavily forested with temperate vegetation than it is at present, but drought‐tolerant xeric vegetation was still widespread along the southern margins of the region. Although human land use may have caused the degradation of land between the mid‐Holocene and the present, the mere presence of xeric vegetation in the Mediterranean region does not require human impact. This challenges the commonly held belief that modern Mediterranean vegetation represents a ‘degraded’ state.
Getting under—and through—the skin: ecological genomics of chytridiomycosis infection in frogs
Authors: BARREIRO L. B. , TUNG J. 
Published: June 2012

Amphibian species around the world are currently becoming endangered or lost at a rate that outstrips other vertebrates—victims of a combination of habitat loss, climate change and susceptibility to emerging infectious disease (Stuart et al. 2004). One of the most devastating such diseases is caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), which infects hundreds of amphibian species on multiple continents. While Bd itself has been characterized for some time, we still know little about the mechanisms that make it so deadly. In this issue of Molecular Ecology, Rosenblum et al. describe a genomic approach to this question, reporting the results of a genome‐wide analysis of the transcriptional response to Bd in the liver, skin and spleen of mountain yellow‐legged frogs (Rana mucosa and R. sierrae: Fig. 1) (Rosenblum et al. 2012). Their results indicate that the skin is not only the first, but likely the most important, line of defence in these animals. Strikingly, they describe a surprisingly modest immune response to infection in Rana, a result that may help explain variable Bd susceptibility across populations and species. The frog and the fungus. Left, the mountain yellow‐legged frog, one of hundreds of worldwide amphibian species in decline. Right, the chytrid fungus Batrachochytrium dendrobatidis (Bd), in part responsible for loss of these frogs. In Rana mucosa and R. sierrae, infection by Bd leads to a massive loss of skin integrity and frequently death. Photo credit: (left panel) Roland A. Knapp, Sierra Nevada Aquatic Research Lab; (right panel) Erica B. Rosenblum, University of Idaho.image
Intestinal microbiota composition in fishes is influenced by host ecology and environment
Authors: WONG SANDI , RAWLS JOHN F. 
Published: June 2012

The digestive tracts of vertebrates are colonized by complex assemblages of micro‐organisms, collectively called the gut microbiota. Recent studies have revealed important contributions of gut microbiota to vertebrate health and disease, stimulating intense interest in understanding how gut microbial communities are assembled and how they impact host fitness (Sekirov et al. 2010). Although all vertebrates harbour a gut microbiota, current information on microbiota composition and function has been derived primarily from mammals. Comparisons of different mammalian species have revealed intriguing associations between gut microbiota composition and host diet, anatomy and phylogeny (Ley et al. 2008b). However, mammals constitute <10% of all vertebrate species, and it remains unclear whether similar associations exist in more diverse and ancient vertebrate lineages such as fish. In this issue, Sullam et al. (2012) make an important contribution toward identifying factors determining gut microbiota composition in fishes. The authors conducted a detailed meta‐analysis of 25 bacterial 16S rRNA gene sequence libraries derived from the intestines of different fish species. To provide a broader context for their analysis, they compared these data sets to a large collection of 16S rRNA gene sequence data sets from diverse free‐living and host‐associated bacterial communities. Their results suggest that variation in gut microbiota composition in fishes is strongly correlated with species habitat salinity, trophic level and possibly taxonomy. Comparison of data sets from fish intestines and other environments revealed that fish gut microbiota compositions are often similar to those of other animals and contain relatively few free‐living environmental bacteria. These results suggest that the gut microbiota composition of fishes is not a simple reflection of the micro‐organisms in their local habitat but may result from host‐specific selective pressures within the gut (Bevins & Salzman 2011).