bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal occurrence and sexual maturation of Japanese pygmy squid (Idiosepius paradoxus) at the northern limits of their distribution
Authors: Sato Noriyosi , Awata Satoshi , Munehara Hiroyuki 
Published: May 2009

AbstractSato, N., Awata, S., and Munehara, H. 2009. Seasonal occurrence and sexual maturation of Japanese pygmy squid (Idiosepius paradoxus) at the northern limits of their distribution. – ICES Journal of Marine Science, 66: 811–815. The distribution of aquatic animals is limited by water temperature. However, little is known about migration patterns, overwintering, and reproduction at the extremities of their distribution. To investigate the sexual maturation of Japanese pygmy squid (Idiosepius paradoxus) and their ability to survive during winter at the northern limits of their distribution, we collected samples monthly at Usujiri in northern Japan and carried out experiments on low-temperature tolerance. Squid were collected during 4 months in autumn and early winter. In autumn, all squid were large and sexually mature, and many egg masses were found on the surface of seagrass, whereas in early winter, only small immature squid were collected. A warm north-flowing current reached the Usujiri area during autumn, so the squid were likely transported by the current and some of the small squid were recruits that hatched there. Field data and the results of experiments on tolerance of the species to low temperatures showed that it cannot survive at the low temperatures around Usujiri in winter. The migration pattern of I. paradoxus may differ from the traditional pattern for marine resources, where young fish are transported passively and do not reproduce at the extremities of their distribution.
Impact of Cropping Sequences and Alternative Hosts on Take-all Management of Winter Wheat in Arkansas
Authors: Milus Eugene A. , Cartwright Richard D. , Rothrock Craig S. , Anders Merle , Slaton Nathan 
Published: May 2009

Cultural practices are the principle means for managing take-all of wheat caused by Gaeumannomyces graminis var. tritici. This research identified cropping sequences that can be used to manage take-all in Arkansas. For dryland fields where the opportunity to grow rotational crops is limited, summer fallow was the best option for managing take-all. For irrigated fields, rotation out of wheat for at least one year reduced incidence and severity of take-all, and rice was the most effective rotational crop. Summer fallow or a rice crop was more detrimental to survival of take-all inoculum compared to corn or soybean. Reductions in inoculum were associated with elevated soil temperatures during the summer in fallow fields and with soil anoxia in flooded rice fields. Managing grassy weeds is important during rotations out of wheat. Rescuegrass was the most susceptible grassy weed to G. graminis var. tritici in this study. Although Italian ryegrass was only moderately susceptible, it likely plays a major role in maintaining inoculum because of its wide distribution and large population size. Accepted for publication 11 April 2009. Published 12 May 2009.
Selective NTPDase2 expression modulates in vivo rat glioma growth
Authors: Braganhol Elizandra , Morrone Fernanda B. , Bernardi Andressa , Huppes Daiane , Meurer Luise , Edelweiss Maria Isabel A. , Lenz Guido , Wink Márcia R. , Robson Simon C. , Battastini Ana Maria O. 
Published: May 2009

The ectonucleoside triphosphate diphosphohydrolases (E‐NTPDases) are a family of ectoenzymes that hydrolyze extracellular nucleotides, thereby modulating purinergic signaling. Gliomas have low expression of all E‐NTPDases, particularly NTPDase2, when compared to astrocytes in culture. Nucleotides induce glioma proliferation and ATP, although potentially neurotoxic, does not evoke cytotoxic action on the majority of glioma cultures. We have previously shown that the co‐injection of apyrase with gliomas decreases glioma progression. Here, we tested whether selective re‐establishment of NTPDase2 expression would affect glioma growth. NTPDase2 overexpression in C6 glioma cells had no effect on in vitro proliferation but dramatically increased tumor growth and malignant characteristics in vivo. Additionally, a sizable platelet sequestration in the tumor area and an increase in CD31 or platelet/endothelial cell adhesion molecule‐1 (PECAM‐1), vascular endothelial growth factor and OX‐42 immunostaining were observed in C6‐Enhanced Yellow Fluorescent Protein (EYFP)/NTPDase2‐derived gliomas when compared to controls. Treatment with clopidogrel, a P2Y12 antagonist with anti‐platelet properties, decreased these parameters to control levels. These data suggest that the ADP derived from NTPDase2 activity stimulates platelet migration to the tumor area and that NTPDase2, by regulating angiogenesis and inflammation, seems to play an important role in tumor progression. In conclusion, our results point to the involvement of purinergic signaling in glioma progression. (Cancer Sci 2009)
Two‐stage focus‐hold system for rapid ultra‐sensitive read‐out of large‐area biochips
Authors: HESCH C. , HESSE J. , JACAK J. , SCHÜTZ G.J. 
Published: May 2009

SummaryWe report here the development of a method for holding the focal plane in a fluorescence‐based biochip scanner. The fast read‐out of large (multiple cm2) glass slides as used in modern chip technology imposes severe constraints on the focal system. The limited focal depth of high‐NA objectives together with the demand for single‐molecule sensitivity challenges traditional focus‐hold systems. Various long‐ and short‐term effects disturb the often multiple hour‐long data‐acquisitioning process and cause blurred or unusable image data. Traditional focus‐hold systems were often limited in terms of range, reaction time, sensitivity or demanded a large number of additional components. Our system uses the back‐reflected illumination beam always present in total internal reflection fluorescence microscopy to generate an error proportional electrical signal, which in turn drives an actuator correcting the objective–sample distance. The latter consists of a fast but range‐limited piezo drive attached to the objective and a slower motor coupled to the microscope's z‐drive. With this combination, fast reaction times and virtually unlimited correction distances are possible. We show the applicability by scanning DNA microarrays on 27 × 18‐mm2 glass slides with single‐molecule sensitivity over the whole array. Single‐fluorescence dyes are imaged as diffraction‐limited spots.
Quantification of colocalization and cross‐talk based on spectral angles
Authors: GAVRILOVIC M. , WÄHLBY C. 
Published: May 2009

SummaryCommon methods for quantification of colocalization in fluorescence microscopy typically require cross‐talk free images or images where cross‐talk has been eliminated by image processing, as they are based on intensity thresholding. Quantification of colocalization includes not only calculating a global measure of the degree of colocalization within an image, but also a classification of each image pixel as showing colocalized signals or not. In this paper, we present a novel, automated method for quantification of colocalization and classification of image pixels. The method, referred to as SpecDec, is based on an algorithm for spectral decomposition of multispectral data borrowed from the field of remote sensing. Pixels are classified based on hue rather than intensity. The hue distribution is presented as a histogram created by a series of steps that compensate for the quantization noise always present in digital image data, and classification rules are thereafter based on the shape of the angle histogram. Detection of colocalized signals is thus only dependent on the hue, making it possible to classify also low‐intensity objects, and decoupling image segmentation from detection of colocalization. Cross‐talk will show up as shifts of the peaks of the histogram, and thus a shift of the classification rules, making the method essentially insensitive to cross‐talk. The method can also be used to quantify and compensate for cross‐talk, independent of the microscope hardware.
Digital enhancement of haematoxylin‐ and eosin‐stained histological images for red–green colour‐blind observers
Authors: LANDINI G. , PERRYER G. 
Published: May 2009

SummaryIndividuals with red–green colour‐blindness (CB) commonly experience great difficulty differentiating between certain histological stain pairs, notably haematoxylin–eosin (H&E). The prevalence of red–green CB is high (6–10% of males), including among medical and laboratory personnel, and raises two major concerns: first, accessibility and equity issues during the education and training of individuals with this disability, and second, the likelihood of errors in critical tasks such as interpreting histological images. Here we show two methods to enhance images of H&E‐stained samples so the differently stained tissues can be well discriminated by red–green CBs while remaining usable by people with normal vision. Method 1 involves rotating and stretching the range of H&E hues in the image to span the perceptual range of the CB observers. Method 2 digitally unmixes the original dyes using colour deconvolution into two separate images and repositions the information into hues that are more distinctly perceived. The benefits of these methods were tested in 36 volunteers with normal vision and 11 with red–green CB using a variety of H&E stained tissue sections paired with their enhanced versions. CB subjects reported they could better perceive the different stains using the enhanced images for 85% of preparations (method 1: 90%, method 2: 73%), compared to the H&E‐stained original images. Many subjects with normal vision also preferred the enhanced images to the original H&E. The results suggest that these colour manipulations confer considerable advantage for those with red–green colour vision deficiency while not disadvantaging people with normal colour vision.
Real‐time and label‐free detection of chloramphenicol residues with specific molecular interaction
Authors: DONG Z. , HUANG G. , XU S. , DENG C. , ZHU J. , CHEN S. , YANG X. , ZHAO S. 
Published: May 2009

SummaryMolecular measurements with specific or non‐specific molecular interaction are usually reported by using different methods. This paper shows a method for small‐molecular label‐free measurements in real time with specific and non‐specific molecular interaction based on surface plasmon resonance. The quantitative measurement of glucose with non‐specific molecular interaction was performed simply to validate our self‐built angle‐dependent surface plasmon resonance system, which showed a good sensitivity and stability, such as that of Fourier transform infrared spectrometer. As application, we present the measurement of chloramphenicol residues with specific molecular interaction employing an indirect competitive immunoreaction by using the same surface plasmon resonance system with a limit of detection about 0.5 ng mL−1, which shows a potential application for food safety.
Molecular phylogeography of European Sciurus vulgaris: refuge within refugia?
Authors: GRILL ANDREA , AMORI GIOVANNI , ALOISE GAETANO , LISI IRENE , TOSI GUIDO , WAUTERS LUCAS A. , RANDI ETTORE 
Published: May 2009

AbstractThe red squirrel (Sciurus vulgaris) is a well‐known forest animal distributed all over Europe. Still, we are far from having a firm knowledge of the species’ phylogeography. This study investigates the genetic differentiation of S. vulgaris across the species’ Eurasian range, using sequence data from the mitochondrial DNA gene (D‐loop, 252 base pairs, cytochrome b, 359 base pairs), and eight variable autosomal microsatellite loci genotyped for 236 individuals. The results reveal the presence of two main mitochondrial phylogroups. The first clade comprises the individuals from the region of Calabria in southern Italy, belonging to the subspecies S. v. meridionalis, while the second clade contains the remainder of the studied individuals. Bayesian analysis of microsatellite genotypes resulted in three main clusterings corresponding to the three S. vulgaris subspecies: infuscatus, meridionalis and fuscoater. Geographical distribution of mtDNA haplotypes and mismatch analysis suggest a common refugium for the red squirrel across most of its present range from which expansion happened rather rapidly. The genotype mixing of italicus with northern populations could be a residual of postglacial expansion. The lack of mixing between the Calabrian lineage and the rest of European red squirrel haplotypes can be seen as evidence for distinct histories throughout the Pleistocene. Calabrian mtDNA probably diverged in an ice age contraction and remained isolated from the neighbouring squirrel populations until very recent times.
Second messenger signalling governs Escherichia coli biofilm induction upon ribosomal stress
Authors: Boehm Alex , Steiner Samuel , Zaehringer Franziska , Casanova Alain , Hamburger Fabienne , Ritz Daniel , Keck Wolfgang , Ackermann Martin , Schirmer Tilman , Jenal Urs 
Published: May 2009

SummaryBiofilms are communities of surface‐attached, matrix‐embedded microbial cells that can resist antimicrobial chemotherapy and contribute to persistent infections. Using an Escherichia coli biofilm model we found that exposure of bacteria to subinhibitory concentrations of ribosome‐targeting antibiotics leads to strong biofilm induction. We present evidence that this effect is elicited by the ribosome in response to translational stress. Biofilm induction involves upregulation of the polysaccharide adhesin poly‐β‐1,6‐N‐acetyl‐glucosamine (poly‐GlcNAc) and two components of the poly‐GlcNAc biosynthesis machinery, PgaA and PgaD. Poly‐GlcNAc control depends on the bacterial signalling molecules guanosine‐bis 3′, 5′(diphosphate) (ppGpp) and bis‐(3′‐5′)‐cyclic di‐GMP (c‐di‐GMP). Treatment with translation inhibitors causes a ppGpp hydrolase (SpoT)‐mediated reduction of ppGpp levels, resulting in specific derepression of PgaA. Maximal induction of PgaD and poly‐GlcNAc synthesis requires the production of c‐di‐GMP by the dedicated diguanylate cyclase YdeH. Our results identify a novel regulatory mechanism that relies on ppGpp signalling to relay information about ribosomal performance to the Pga machinery, thereby inducing adhesin production and biofilm formation. Based on the important synergistic roles of ppGpp and c‐di‐GMP in this process, we suggest that interference with bacterial second messenger signalling might represent an effective means for biofilm control during chronic infections.
Filariasis and lymphoedema
Authors: PFARR K. M. , DEBRAH A. Y. , SPECHT S. , HOERAUF A. 
Published: May 2009

SummaryAmong the causes of lymphoedema (LE), secondary LE due to filariasis is the most prevalent. It affects only a minority of the 120 million people infected with the causative organisms of lymphatic filariasis (LF), Wuchereria bancrofti and Brugia malayi/timori, but is clustered in families, indicating a genetic basis for development of this pathology. The majority of infected individuals develop filarial‐specific immunosuppression that starts even before birth in cases where mothers are infected and is characterized by regulatory T‐cell responses and high levels of IgG4, thus tolerating high parasite loads and microfilaraemia. In contrast, individuals with this pathology show stronger immune reactions biased towards Th1, Th2 and probably also Th17. Importantly, as for the aberrant lymph vessel development, innate immune responses that are triggered by the filarial antigen ultimately result in the activation of vascular endothelial growth factors (VEGF), thus promoting lymph vessel hyperplasia as a first step to lymphoedema development. Wolbachia endosymbionts are major inducers of these responses in vitro, and their depletion by doxycycline in LF patients reduces plasma VEGF and soluble VEGF‐receptor‐3 levels to those seen in endemic normals preceding pathology improvement. The search for the immunogenetic basis for LE could lead to the identification of risk factors and thus, to prevention; and has so far led to the identification of single‐nucleotide polymorphisms (SNP) with potential functional relevance to VEGF, cytokine and toll‐like receptor (TLR) genes. Hydrocele, a pathology with some similarity to LE in which both lymph vessel dilation and lymph extravasation are shared sequelae, has been found to be strongly associated with a VEGF‐A SNP known for upregulation of this (lymph‐)angiogenesis factor.
Functional loss of pAMT results in biosynthesis of capsinoids, capsaicinoid analogs, in Capsicum annuum cv. CH‐19 Sweet
Authors: Lang Yaqin , Kisaka Hiroaki , Sugiyama Ryuji , Nomura Kenzo , Morita Akihito , Watanabe Tatsuo , Tanaka Yoshiyuki , Yazawa Susumu , Miwa Tetsuya 
Published: May 2009

SummaryCapsaicinoids are responsible for the spicy flavor of pungent peppers (Capsicum). The cultivar CH‐19 Sweet is a non‐pungent pepper mutant derived from a pungent pepper strain, Capsicum annuum CH‐19. CH‐19 Sweet biosynthesizes capsaicinoid analogs, capsinoids. We determined the genetic and metabolic mechanisms of capsinoid biosynthesis in this cultivar. We analyzed the putative aminotransferase (pAMT) that is thought to catalyze the formation of vanillylamine from vanillin in the capsaicinoid biosynthetic pathway. Enzyme assays revealed that pAMT activity catalyzing vanillylamine formation was completely lost in CH‐19 Sweet placenta tissue. RT‐PCR analysis showed normal mRNA transcription of the pAMT gene; however, SNP analysis of the cDNA sequence showed a T nucleotide insertion at 1291 bp in the pAMT gene of CH‐19 Sweet. This insertion formed a new stop codon, TGA, that prevented normal translation of the gene, and the pAMT protein did not accumulate in CH‐19 Sweet as determined using Western blot analysis. We developed a dCAPS marker based on the T insertion in the pAMT gene of CH‐19 Sweet, and showed that the pAMT genotype co‐segregated with the capsinoid or capsaicinoid fruit phenotype in the F2 population. The T insertion was not found in other pungent and non‐pungent Capsicum lines, suggesting that it is specific to CH‐19 Sweet. CH‐19 Sweet’s pAMT gene mutation is an example of a nonsense mutation in a single gene that alters a secondary metabolite biosynthetic pathway, resulting in the biosynthesis of analogs. The dCAPS marker will be useful in selecting lines with capsinoid‐containing fruits in pepper‐breeding programs.
Detailed analysis of the DNA recognition motifs of the Xanthomonas type III effectors AvrBs3 and AvrBs3Δrep16
Authors: Kay Sabine , Hahn Simone , Marois Eric , Wieduwild Robert , Bonas Ulla 
Published: May 2009

SummaryThe Gram‐negative phytopathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv) employs a type III secretion system to translocate effector proteins into plant cells where they modulate host signaling pathways to the pathogen’s benefit. The effector protein AvrBs3 acts as a eukaryotic transcription factor and induces the expression of plant genes termed UPA (up‐regulated by AvrBs3). Here, we describe 11 new UPA genes from bell pepper that are induced by AvrBs3 early after infection with Xcv. Sequence comparisons revealed the presence of a conserved AvrBs3‐responsive element, the UPA box, in all UPA gene promoters analyzed. Analyses of UPA box mutant derivatives confirmed its importance for gene induction by AvrBs3. We show that DNA binding and gene activation were strictly correlated. DNase I footprint studies demonstrated that the UPA box corresponds to the center of the AvrBs3‐protected DNA region. Type III delivery of AvrBs3 and mutant derivatives showed that some UPA genes are induced by the AvrBs3 deletion derivative AvrBs3Δrep16, which lacks four repeats. We show that AvrBs3Δrep16 recognizes a mutated UPA box with two nucleotide exchanges in positions that are not essential for binding and activation by AvrBs3.
Potassium and Silicon Improve Yield and Juice Quality in Sugarcane (Saccharum officinarum L.) under Salt Stress
Authors: Ashraf M. , Rahmatullah  , Ahmad R. , Afzal M. , Tahir M. A. , Kanwal S. , Maqsood M. A. 
Published: May 2009

AbstractSoil salinity is a major abiotic stress which adversely affects the yield and juice quality in sugarcane. However, the mineral nutrient status of plant plays a crucial role in increasing plant tolerance to salinity. We investigated the effects of K and/or Si on plant growth, yield and juice quality in two sugarcane genotypes differing in salinity tolerance. Addition of K and Si significantly (P ≤ 0.05) increased K and Si concentrations and decreased the accumulation of Na+ in plants under salt stress. Cane yield and yield attributes were significantly (P ≤ 0.05) higher where K and Si were added. Juice quality characteristics like Brix (% soluble solids in juice), Pol (% sucrose in juice), commercial cane sugar (CCS) and sugar recovery in both sugarcane genotypes were also significantly (P ≤ 0.05) improved with the supplementation of K and Si. For most of the growth parameters, it was found that K either alone or in combination with Si was more effective to alleviate salt stress in both sugarcane genotypes than Si alone. Moreover, the beneficial effects of K and Si were more pronounced in salt sensitive genotype than in salt tolerant genotype. The results suggested that K and Si counteracted the deleterious effects of high salinity/sodicity in sugarcane by lowering the accumulation of Na+ and increase in K+ concentration with a resultant improvement in K+/Na+ ratio which is a good indicator to assess plant tolerance to salinity.
Genetic diversity and population structure of the golden cuttlefish,Sepia esculenta(Cephalopoda: Sepiidae) indicated by microsatellite DNA variations
Authors: Zheng Xiaodong , Ikeda Minoru , Kong Lingfeng , Lin Xiangzhi , Li Qi , Taniguchi Nobuhiko 
Published: May 2009

AbstractThe golden cuttlefish,Sepia esculentaHoyle, 1885 (Cephalopoda: Sepiidae) is a valuable and important fishery resource for China, Japan and Korea. This fishery has experienced severe population decline largely due to overexploitation in past decades. To provide guidelines for fisheries management, we estimated genetic diversity and population structure across four locations along the coast of Japan and one location in China (a total 281 individuals) using nine microsatellite DNA loci.Sepia esculentashowed high genetic variability with mean allele richness ranging from 15.8 to 21.4, and mean heterozygosity from 0.80 to 0.90. Weak but significant genetic differentiation was present and theFSTvalue was 0.020 across all five populations. The useful information obtained in this study will offer insights into how to fine‐tune conservation and fishery management measures for this species and resource in the future.