bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of small RNAs, degradome and transcriptome sequencing in hyperaccumulator Sedum alfredii uncovers a complex regulatory network and provides insights into cadmium phytoremediation
Authors: Han Xiaojiao , Yin Hengfu , Song Xixi , Zhang Yunxing , Liu Mingying , Sang Jiang , jiang Jing , Li Jihong , Zhuo Renying 
Published: January 2016

SummaryThe hyperaccumulating ecotype of Sedum alfredii Hance is a cadmium (Cd)/zinc/lead co‐hyperaccumulating species of Crassulaceae. It is a promising phytoremediation candidate accumulating substantial heavy metal ions without obvious signs of poisoning. However, few studies have focused on the regulatory roles of miRNAs and their targets in the hyperaccumulating ecotype of S. alfredii. Here, we combined analyses of the transcriptomics, sRNAs and the degradome to generate a comprehensive resource focused on identifying key regulatory miRNA‐target circuits under Cd stress. A total of 87 721 unigenes and 356 miRNAs were identified by deep sequencing, and 79 miRNAs were differentially expressed under Cd stress. Furthermore, 754 target genes of 194 miRNAs were validated by degradome sequencing. A gene ontology (GO) enrichment analysis of differential miRNA targets revealed that auxin, redox‐related secondary metabolism and metal transport pathways responded to Cd stress. An integrated analysis uncovered 39 pairs of miRNA targets that displayed negatively correlated expression profiles. Ten miRNA‐target pairs also exhibited negative correlations according to a real‐time quantitative PCR analysis. Moreover, a coexpression regulatory network was constructed based on profiles of differentially expressed genes. Two hub genes, ARF4 (auxin response factor 4) and AAP3 (amino acid permease 3), which might play central roles in the regulation of Cd‐responsive genes, were uncovered. These results suggest that comprehensive analyses of the transcriptomics, sRNAs and the degradome provided a useful platform for investigating Cd hyperaccumulation in S. alfredii, and may provide new insights into the genetic engineering of phytoremediation.
Effects of Arrangement of UV Light‐Emitting Diodes on the Inactivation Efficiency of Microorganisms in Water
Authors: Oguma Kumiko , Kita Ryo , Takizawa Satoshi 
Published: January 2016

AbstractUltraviolet light‐emitting diodes (UV‐LEDs) offer high flexibility in the reactor design for water disinfection. To specify the key design factors affecting the performance of a reactor, we examined how the arrangement of UV‐LEDs in a cylindrical reactor affects the inactivation efficiency of Escherichia coli and coliphage Qβ. A ring‐shaped UV‐LED apparatus, composed of two units containing ten 285‐nm UV‐LEDs each, were attached to a quartz cylinder, and microbial suspensions flowed through the cylinder for single pass at altered flow rates. The distance between the two units, L, was altered to examine its effects on inactivation efficiencies. Over 4 log inactivation of E. coli was achieved at 800 mL min−1 regardless of the L values, suggesting that the apparatus has a high potential to disinfect water. The inactivation at L = 20 mm was significantly higher than that at L = 0 in all cases tested (ANOVA, P < 0.05), while this was not true when L was extended to 40 and 60 mm. Therefore, a separate arrangement of UV‐LEDs at a certain distance can improve the efficiency, and the distance matters to enhance the performance. This study involves a design concept on how to arrange UV‐LEDs in a water disinfection apparatus.
Carbon dioxide emission from bamboo culms
Authors: Zachariah E. J. , Sabulal B. , Nair D. N. K. , Johnson A. J. , Kumar C. S. P. 
Published: January 2016

AbstractBamboos are one of the fastest growing plants on Earth, and are widely considered to have high ability to capture and sequester atmospheric carbon, and consequently to mitigate climate change. We tested this hypothesis by measuring carbon dioxide (CO2) emissions from bamboo culms and comparing them with their biomass sequestration potential. We analysed diurnal effluxes from Bambusa vulgaris culm surface and gas mixtures inside hollow sections of various bamboos using gas chromatography. Corresponding variations in gas pressure inside the bamboo section and culm surface temperature were measured. SEM micrographs of rhizome and bud portions of bamboo culms were also recorded. We found very high CO2 effluxes from culm surface, nodes and buds of bamboos. Positive gas pressure and very high concentrations of CO2 were observed inside hollow sections of bamboos. The CO2 effluxes observed from bamboos were very high compared to their carbon sequestration potential. Our measurements suggest that bamboos are net emitters of CO2 during their lifespan.
Beach erosion under rising sea‐level modulated by coastal geomorphology and sediment availability on carbonate reef‐fringed island coasts
Authors: Romine Bradley M. , Fletcher Charles H. , Frazer L. Neil , Anderson Tiffany R. 
Published: January 2016

AbstractThis study addresses gaps in understanding the relative roles of sea‐level change, coastal geomorphology and sediment availability in driving beach erosion at the scale of individual beaches. Patterns of historical shoreline change are examined for spatial relationships to geomorphology and for temporal relationships to late‐Holocene and modern sea‐level change. The study area shoreline on the north‐east coast of Oahu, Hawaii, is characterized by a series of kilometre‐long beaches with repeated headland‐embayed morphology fronted by a carbonate fringing reef. The beaches are the seaward edge of a carbonate sand‐rich coastal strand plain, a common morphological setting in tectonically stable tropical island coasts. Multiple lines of geological evidence indicate that the strand plain prograded atop a fringing reef platform during a period of late‐Holocene sea‐level fall. Analysis of historical shoreline changes indicates an overall trend of erosion (shoreline recession) along headland sections of beach and an overall trend of stable to accreting beaches along adjoining embayed sections. Eighty‐eight per cent of headland beaches eroded over the past century at an average rate of −0·12 ± 0·03 m yr−1. In contrast, 56% of embayed beaches accreted at an average rate of 0·04 ± 0·03 m yr−1. Given over a century of global (and local) sea‐level rise, the data indicate that embayed beaches are showing remarkable resiliency. The pattern of headland beach erosion and stable to accreting embayments suggests a shift from accretion to erosion particular to the headland beaches with the initiation of modern sea‐level rise. These results emphasize the need to account for localized variations in beach erosion related to geomorphology and alongshore sediment transport in attempting to forecast future shoreline change under increasing sea‐level rise.
Foot contact angle variability during a prolonged run with relation to injury history and habitual foot strike pattern
Authors: Paquette M. R. , Milner C. E. , Melcher D. A. 
Published: January 2016

Foot strike pattern and movement variability have each been associated with running injuries. Foot contact angle (FCA) is a common measure of strike pattern. Thus, variability in FCA could be an important running injury risk factor. The purposes of this study were to compare (a) foot contact angle (FCA) and its variability between runners with and without injury history and, (b) FCA variability between habitual rearfoot strike (RFS) and non‐RFS runners during a prolonged run. Twenty‐three runners with and 21 without injury history participated. Motion capture was used to collect kinematic data during a 40 min treadmill run. Average FCA and its variability were compared between injury groups and among four time points. FCA and its variability were not different between runners with and without injury history or among time points during the run. FCA variability was lower in non‐RFS compared to RFS runners (P < 0.001). Lower FCA variability in non‐RFS runners may have implications for higher injury risks due to repeated localized tissue loading. Prospective analyses on the effects of lower FCA variability on injury risk are needed.
The crustal evolution of South America from a zircon Hf‐isotope perspective
Authors: Augustsson Carita , Willner Arne P. , Rüsing Tobias , Niemeyer Hans , Gerdes Axel , Adams Christopher J. , Miller Hubert 
Published: January 2016

AbstractHf‐isotope data of >1100 detrital zircon grains from the Palaeozoic, south‐central Andean Gondwana margin record the complete crustal evolution of South America, which was the predominant source. The oldest grains, with crustal residence ages of 3.8–4.0 Ga, are consistent with complete recycling of existing continental crust around 4 Ga. We confirm three major Archaean, Palaeoproterozoic (Transamazonian) and late Mesoproterozoic to early Neoproterozoic crust‐addition phases as well as six igneous phases during Proterozoic to Palaeozoic time involving mixing of juvenile and crustally reworked material. A late Mesoproterozoic to early Neoproterozoic, Grenville‐age igneous belt can be postulated along the palaeo‐margin of South America. This belt was the basement for later magmatic arcs and accreted allochthonous microcontinents as recorded by similar crustal residence ages. Crustal reworking likely dominated over juvenile addition during the Palaeozoic era, and Proterozoic and Archaean zircon was mainly crustally reworked from the eroding, thickened Ordovician Famatinian arc.
A common miRNA160‐based mechanism regulates ovary patterning, floral organ abscission and lamina outgrowth in tomato
Authors: Damodharan Subha , Zhao Dazhong , Arazi Tzahi 
Published: January 2016

SummaryPlant microRNAs play vital roles in auxin signaling via the negative regulation of auxin response factors (ARFs). Studies have shown that targeting of ARF10/16/17 by miR160 is indispensable for various aspects of development, but its functions in the model crop tomato (Solanum lycopersicum) are unknown. Here we knocked down miR160 (sly–miR160) using a short tandem target mimic (STTM160), and investigated its roles in tomato development. Northern blot analysis showed that miR160 is abundant in developing ovaries. In line with this, its down‐regulation perturbed ovary patterning as indicated by the excessive elongation of the proximal ends of mutant ovaries and thinning of the placenta. Following fertilization, these morphological changes led to formation of elongated, pear‐shaped fruits reminiscent of those of the tomato ovate mutant. In addition, STTM160‐expressing plants displayed abnormal floral organ abscission, and produced leaves, sepals and petals with diminished blades, indicating a requirement for sly–miR160 for these auxin‐mediated processes. We found that sly–miR160 depletion was always associated with the up‐regulation of SlARF10A, SlARF10B and SlARF17, of which the expression of SlARF10A increased the most. Despite the sly–miR160 legitimate site of SlARF16A, its mRNA levels did not change in response to sly–miR160 down‐regulation, suggesting that it may be regulated by a mechanism other than mRNA cleavage. SlARF10A and SlARF17 were previously suggested to function as inhibiting ARFs. We propose that by adjusting the expression of a group of ARF repressors, of which SlARF10A is a primary target, sly–miR160 regulates auxin‐mediated ovary patterning as well as floral organ abscission and lateral organ lamina outgrowth.
Cytomegalovirus in Australian blood donors: seroepidemiology and seronegative red blood cell component inventories
Authors: Lancini Daniel V. , Faddy Helen M. , Ismay Sue , Chesneau Stuart , Hogan Chris , Flower Robert L. 
Published: January 2016

BACKGROUNDCytomegalovirus (CMV) can lead to severe disease in high‐risk subpopulations. To prevent transfusion‐transmitted CMV in these patient groups, the Australian Red Cross Blood Service maintains inventories of CMV‐seronegative fresh blood components.STUDY DESIGN AND METHODSDonor demographic data and CMV seroscreening results for all blood donations and blood components issued in Australia between financial years (FYs) 2008/09 to 2012/13 inclusive were obtained. Population estimates were also extracted for the calculation of age‐weighted seroprevalence estimates. Linear regression was used to model trends in red blood cell (RBC) component acquisition and demand.RESULTSThe estimated age‐weighted seroprevalence of CMV in 20‐ to 69‐year old Australians was 76.12 ± 0.13%, with higher seroprevalence in females and older age groups. Seroprevalence decreased over the study period, while the demand for CMV‐seronegative RBC components increased. It was predicted that component acquisition may be insufficient by FY 2017/18 if current trends persist.CONCLUSIONThese findings represent an evaluation of CMV seroepidemiology in Australia and form a basis to predict the future status of CMV‐seronegative RBC component inventories. The results will serve to guide Blood Service operations and inform current international debate on CMV‐safe blood components.
Differentiation between dogs with thrombosis and normal dogs using the overall hemostasis potential assay
Authors: Dengate Anna L. , Morel‐Kopp Marie‐Christine , Beatty Julia A. , Barrs Vanessa , Braddock Jody A. , Churcher Richard K. , Wilson Bethany J. , Ward Christopher M. 
Published: January 2016

AbstractObjectiveTo determine whether the overall hemostasis potential (OHP) and calibrated automated thrombogram (CAT) were significantly different between dogs with thrombosis and normal dogs.AnimalsTen dogs with clinical evidence of thromboembolic disease had both OHP and CAT performed. Forty healthy control dogs had OHP performed, and 23 of these also had CAT performed.Measurements and Main ResultsDogs with thrombosis had significantly higher OHP (P = 0.003), overall coagulation potential (P = 0.0001), and maximum optical density (Max OD, P < 0.0001) than normal dogs, and a significantly longer delay in the start of clot formation (P = 0.01). Max OD was higher than established reference intervals in 80% of the dogs with thrombosis. Using the CAT assay, dogs with thrombosis had a significantly longer lag time than normal dogs (P < 0.001). Plasma fibrinogen concentration correlated positively with overall coagulation potential, OHP, Max OD, and the slope of the OHP curve (P < 0.05), and was increased in 90% of dogs with thrombosis.ConclusionsThe OHP assay findings were significantly different between normal dogs and those with thrombosis. CAT did not detect any significant differences between these populations of dogs, other than the lag time of the assay.
Histologic and immunohistochemical predictors of clinical behavior for feline diffuse iris melanoma
Authors: Wiggans K. Tomo , Reilly Christopher M. , Kass Philip H. , Maggs David J. 
Published: January 2016

AbstractObjectiveTo determine histologic and immunohistochemical predictors of metastasis of feline diffuse iris melanoma (FDIM).AnimalsGlobes from 47 client‐owned cats enucleated for FDIM between January 1985 and December 2013.ProceduresHematoxylin and eosin‐stained sections were evaluated for neoplastic invasiveness and cell morphology, necrosis within the neoplasm, inflammation, and glaucoma. Sections were immunolabeled with antibodies against melan‐A, PNL2, E‐cadherin, or B‐Raf, and label intensity, percentage of labeled cells, and label homogeneity were semi‐quantitatively graded. Medical records were evaluated, and referring veterinarians and clients were contacted to determine whether cats developed metastasis following enucleation. The log‐rank test or Cox proportional hazards model was used to determine associations between histologic or immunohistochemical parameters and metastasis.ResultsMetastasis was suspected or confirmed in 9/47 (19%) cats. Extrascleral extension, necrosis within the neoplasm, a mitotic index of >7 mitoses in 10 high‐power (×400) fields, choroidal invasion, and increased E‐cadherin and melan‐A label intensity were each associated with increased rate of metastasis. PNL2 label homogeneity was associated with decreased rate of metastasis. Decreased PNL2 label intensity and an increasing percentage of neoplastic cells labeled for melan‐A each approached significance for increased rate of metastasis.ConclusionsWe report four histologic and three immunohistochemical parameters helpful in determining cats at risk of metastasis of FDIM. Further studies should determine if B‐Raf mutations identified in human malignant melanomas are found in cats with FDIM and assess benefits of adjunctive therapy following enucleation of eyes with FDIM bearing poor prognostic indicators.
Three‐dimensional printing of orbital and peri‐orbital masses in three dogs and its potential applications in veterinary ophthalmology
Authors: Dorbandt Daniel M. , Joslyn Stephen K. , Hamor Ralph E. 
Published: January 2016

AbstractObjectiveTo describe the technique and utility of three‐dimensional (3D) printing for orbital and peri‐orbital masses and discuss other potential applications for 3D printing.Animals studiedThree dogs with a chronic history of nonpainful exophthalmos.ProceduresComputed tomography (CT) and subsequent 3D printing of the head was performed on each case. CT confirmed a confined mass, and an ultrasound‐guided biopsy was obtained in each circumstance. An orbitotomy was tentatively planned for each case, and a 3D print of each head with the associated globe and mass was created to assist in surgical planning.ResultsIn case 1, the mass was located in the cranioventral aspect of the right orbit, and the histopathologic diagnosis was adenoma. In case 2, the mass was located within the lateral masseter muscle, ventral to the right orbit between the zygomatic arch and the ramus of the mandible. The histopathologic diagnosis in case 2 was consistent with a lipoma. In case 3, the mass was located in the ventral orbit, and the histopathologic diagnosis was histiocytic cellular infiltrate.ConclusionsThree‐dimensional printing in cases with orbital and peri‐orbital masses has exceptional potential for improved surgical planning and provides another modality for visualization to help veterinarians, students, and owners understand distribution of disease. Additionally, as the techniques of 3D printing continue to evolve, the potential exists to revolutionize ocular surgery and drug delivery.
Molecular Structural Basis for the Cold Adaptedness of the Psychrophilic β-Glucosidase BglU in Micrococcus antarcticus
Authors: Miao Li-Li , Hou Yan-Jie , Fan Hong-Xia , Qu Jie , Qi Chao , Liu Ying , Li De-Feng , Liu Zhi-Pei 
Published: January 2016

ABSTRACT

Psychrophilic enzymes play crucial roles in cold adaptation of microbes and provide useful models for studies of protein evolution, folding, and dynamic properties. We examined the crystal structure (2.2-Å resolution) of the psychrophilic β-glucosidase BglU, a member of the glycosyl hydrolase 1 (GH1) enzyme family found in the cold-adapted bacterium
Micrococcus antarcticus
. Structural comparison and sequence alignment between BglU and its mesophilic and thermophilic counterpart enzymes (BglB and GlyTn, respectively) revealed two notable features distinct to BglU: (i) a unique long-loop L3 (35 versus 7 amino acids in others) involved in substrate binding and (ii) a unique amino acid, His299 (Tyr in others), involved in the stabilization of an ordered water molecule chain. Shortening of loop L3 to 25 amino acids reduced low-temperature catalytic activity, substrate-binding ability, the optimal temperature, and the melting temperature (

T
m

). Mutation of His299 to Tyr increased the optimal temperature, the

T
m

, and the catalytic activity. Conversely, mutation of Tyr301 to His in BglB caused a reduction in catalytic activity, thermostability, and the optimal temperature (45 to 35°C). Loop L3 shortening and H299Y substitution jointly restored enzyme activity to the level of BglU, but at moderate temperatures. Our findings indicate that loop L3 controls the level of catalytic activity at low temperatures, residue His299 is responsible for thermolability (particularly heat lability of the active center), and long-loop L3 and His299 are jointly responsible for the psychrophilic properties. The described structural basis for the cold adaptedness of BglU will be helpful for structure-based engineering of new cold-adapted enzymes and for the production of mutants useful in a variety of industrial processes at different temperatures.
Improvement of Biological Indicators by Uniformly Distributing Bacillus subtilis Spores in Monolayers To Evaluate Enhanced Spore Decontamination Technologies
Authors: Raguse Marina , Fiebrandt Marcel , Stapelmann Katharina , Madela Kazimierz , Laue Michael , Lackmann Jan-Wilm , Thwaite Joanne E. , Setlow Peter , Awakowicz Peter , Moeller Ralf 
Published: January 2016

ABSTRACT

Novel decontamination technologies, including cold low-pressure plasma and blue light (400 nm), are promising alternatives to conventional surface decontamination methods. However, the standardization of the assessment of such sterilization processes remains to be accomplished. Bacterial endospores of the genera
Bacillus
and
Geobacillus
are frequently used as biological indicators (BIs) of sterility. Ensuring standardized and reproducible BIs for reliable testing procedures is a significant problem in industrial settings. In this study, an electrically driven spray deposition device was developed, allowing fast, reproducible, and homogeneous preparation of
Bacillus subtilis
168 spore monolayers on glass surfaces. A detailed description of the structural design as well as the operating principle of the spraying device is given. The reproducible formation of spore monolayers of up to 5 × 10
7
spores per sample was verified by scanning electron microscopy. Surface inactivation studies revealed that monolayered spores were inactivated by UV-C (254 nm), low-pressure argon plasma (500 W, 10 Pa, 100 standard cubic cm per min), and blue light (400 nm) significantly faster than multilayered spores were. We have thus succeeded in the uniform preparation of reproducible, highly concentrated spore monolayers with the potential to generate BIs for a variety of nonpenetrating surface decontamination techniques.