bluuebunny/crossref_metadata_2025 huggingface dataset:
Issues of Management of Swallowing and Feeding Disorders in the School Setting
Authors: Homer Emily M.
Published: October 2009

Purpose: The purpose of this article is to provide information and suggestions for the logistical management of swallowing and feeding disorders in the schools to school-based speech-language pathologists (SLPs).

Method: A school district in Louisiana has been successfully addressing dysphagia using an interdisciplinary team since 1997. The information presented in this article is the result of the experience and knowledge that has been gained.

Conclusion: A school district can successfully address swallowing and feeding disorders by establishing a team procedure that becomes part of their policy manual. The experiences of established teams can help districts in the beginning stages of developing their teams. Information on issues, such as team models, documentation and paperwork, parent/caregiver cooperation, medical collaboration, and diet preparation can assist SLPs in managing dysphagia in his or her schools.
Picosecond time resolution for electron diffraction
Authors: Schwarzschild Bertram M.
Published: October 2009

Gerard Mourou and Steven Williamson at the University of Rochester have reported the demonstration of a new technique that makes possible the direct observation of laser-induced structural changes and phase transitions in a crystal lattice on a picosecond time scale. They have been able to observe electron diffraction patterns with electron bursts photoelectrically generated by 30-picosecond laser pulses. With this technique Mourou sees no impediment to the production of electron diffraction patterns time resolved to a few hundred femtoseconds.
Laser-driven electron–positron colliders
Authors: Schwarzschild Bertram M.
Published: October 2009

By 1987, two very large colliding-beam accelerators, LEP at CERN and SLC at SLAC, should be providing high-energy physicists with 100-GeV collisions of electrons and positrons. But what of the next generation? With the 27-km-circumference LEP storage ring costing about $400 million and consuming as much electrical power as a city of 150 000 souls, can one really afford to build significantly larger e−e+ accelerators at the turn of the next century?
Relativistic treatment of low-energy nuclear phenomena
Authors: Schwarzschild Bertram M.
Published: October 2009

Because the binding energies of nuclei are very much smaller than their rest masses, one would not have expected relativistic effects to play a significant role in nuclear structure or nuclear scattering at modest energies. Thus the nonrelativistic Schrödinger equation has until recently been the basis for almost all calculations in traditional nuclear physics. But in the past three years, the coming together of precise new data and novel theoretical approaches has made it appear that a fully relativistic treatment is indispensable for the understanding of nuclear phenomena even at low energies.
Modifying materials by intercalation
Authors: Dresselhaus Mildred S.
Published: October 2009

For the past decade, materials research has focused on synthesizing new materials and generating new structural arrangements that exhibit specific desired properties. Some of the greatest advances in this area have come out of work on intercalation compounds, which are formed by the insertion of atomic or molecular layers of a guest chemical species—an intercalant—between layers in a host material. Figure 1 illustrates the basic structure of intercalation compounds. Part a of the figure depicts graphite intercalated with lithium; this structure is described as “commensurate,” because the atoms in each layer of guest material are in registry with those in the neighboring layers of the host material. Part b of the figure shows the incommensurate nature of graphite intercalated with ferric chloride. Although graphite intercalation compounds have been synthesized for over 150 years, it is only very recently that methods have been perfected to the point that one can prepare materials with specific structures and properties. These advances in materials synthesis, coupled with current theoretical interest in two-dimensional physics, have contributed to the current high level of interest in graphite intercalation compounds.
Engineering limits on computer performance
Authors: Seitz Charles L. , Matisoo Juri
Published: October 2009

Although the title of our article addresses engineering limits, we do not mean to convey a grim outlook. Over the past 20 years, the technology of computer systems has advanced dramatically in terms of performance, cost and reliability. There is every reason to expect this advance to continue, at a rate almost as shocking as we have experienced to date. However, the advance already achieved has pushed the mechanisms of switching, storage and communication close enough to fundamental physical limits to bring into awareness for the first time limitations in the engineering of high-performance systems.
Algorithms for concurrent processors
Authors: Fox Geoffrey C. , Otto Steve W.
Published: October 2009

We are on the verge of a revolution in computing, spawned by advances in computer technology. Progress in very-large-scale integration is leading not so much to faster computers, but to much less expensive and much smaller computers—computers contained on a few chips. These machines, whose cost-effectiveness is expected to be staggering, will make it practical to build very-high-performance computers, or “supercomputers,” consisting of very many small computers combined to form a single concurrent processor.
High magnetic fields for physics
Authors: Rubin Lawrence G. , Wolff Peter A.
Published: October 2009

For many years magnetic fields have served as an essential tool of the experimental physicist. For example, in solid-state physics our current understanding of the Fermi surfaces of metals, the band structures of semiconductors, the phases of magnets and the properties of superconductors is in each instance based on observations that involve magnetic fields. Yet, until 25 years ago, the highest dc field available to most scientists was that provided by iron-cored electromagnets—about 3 T (30 kG) in air gaps of a few centimeters. In 1960 the Francis Bitter National Magnetic Laboratory was established to develop magnetic field facilities beyond 3 T and use them for solid-state physics research. The Magnet Lab was the first center for research on high magnetic fields in the world and remains the focus for such work in the United States.
Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli
Authors: Ogura Yoshitoshi , Ooka Tadasuke , Iguchi Atsushi , Toh Hidehiro , Asadulghani Md , Oshima Kenshiro , Kodama Toshio , Abe Hiroyuki , Nakayama Keisuke , Kurokawa Ken , Tobe Toru , Hattori Masahira , Hayashi Tetsuya
Published: October 2009

Among the various pathogenic
Escherichia coli
strains, enterohemorrhagic
E. coli
(EHEC) is the most devastating. Although serotype O157:H7 strains are the most prevalent, strains of different serotypes also possess similar pathogenic potential. Here, we present the results of a genomic comparison between EHECs of serotype O157, O26, O111, and O103, as well as 21 other, fully sequenced
E. coli/Shigella
strains. All EHECs have much larger genomes (5.5–5.9 Mb) than the other strains and contain surprisingly large numbers of prophages and integrative elements (IEs). The gene contents of the 4 EHECs do not follow the phylogenetic relationships of the strains, and they share virulence genes for Shiga toxins and many other factors. We found many lambdoid phages, IEs, and virulence plasmids that carry the same or similar virulence genes but have distinct evolutionary histories, indicating that independent acquisition of these mobile genetic elements has driven the evolution of each EHEC. Particularly interesting is the evolution of the type III secretion system (T3SS). We found that the T3SS of EHECs is composed of genes that were introduced by 3 different types of genetic elements: an IE referred to as the locus of enterocyte effacement, which encodes a central part of the T3SS; SpLE3-like IEs; and lambdoid phages carrying numerous T3SS effector genes and other T3SS-related genes. Our data demonstrate how
E. coli
strains of different phylogenies can independently evolve into EHECs, providing unique insights into the mechanisms underlying the parallel evolution of complex virulence systems in bacteria.
Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis
Authors: Sambriski E. J. , Schwartz D. C. , de Pablo J. J.
Published: October 2009

DNA hybridization plays a central role in biology and, increasingly, in materials science. Yet, there is no precedent for examining the pathways by which specific single-stranded DNA sequences interact to assemble into a double helix. A detailed model of DNA is adopted in this work to examine such pathways and to determine the role of sequence, if any, on DNA hybridization. Transition path sampling simulations reveal that DNA rehybridization is prompted by a distinct nucleation event involving molecular sites with approximately four bases pairing with partners slightly offset from those involved in ideal duplexation. Nucleation is promoted in regions with repetitive base pair sequence motifs, which yield multiple possibilities for finding complementary base partners. Repetitive sequences follow a nonspecific pathway to renaturation consistent with a molecular “slithering” mechanism, whereas random sequences favor a restrictive pathway involving the formation of key base pairs before renaturation fully ensues.
2D IR provides evidence for mobile water molecules in β-amyloid fibrils
Authors: Kim Yung Sam , Liu Liu , Axelsen Paul H. , Hochstrasser Robin M.
Published: October 2009

The motion of water molecules close to amide groups causes their vibrational frequencies to vary rapidly in time. These variations are uniquely sensed by 2-dimensional infrared spectroscopy (2D IR). Here, it is proposed from 2-dimensional experiments on fibrils of amyloid β (Aβ)40 that there are water molecules in the fibrils. The spatial locations of the water (D
2
O) were inferred from the responses of 18 amide modes of Aβ40 labeled with
13
C =
18
O. Fast frequency variations were found for residues L17 and V18 and for the apposed residues L34 and V36, suggesting cavities or channels containing mobile water molecules can form between the 2 sheets. Spectroscopic analysis showed that there are 1.2 water molecules per strand in the fibrils. The
13
C =
18
O substitution of 1 residue per strand creates a linear array of isotopologs along the fibril axis that manifests clearly identifiable vibrational transitions. Here, it is shown from the distributions of amide-I′ vibrational frequencies that the regularity of these chains is strongly residue dependent and in most cases the distorted regions are also those associated with the putative mobile water molecules. It is proposed that Aβ40 fibrils contain structurally significant mobile water molecules within the intersheet region.
Immunobiology of mild micronutrient deficiencies
Authors: Bhaskaram P.
Published: October 2009

Nutrition is a critical determinant of the outcome of host microbe interactions through a modulation of the immune response. Besides macronutrient malnutrition, deficiencies of several macronutrients also influence immune homeostasis and thus affect infection-related morbidity and mortality. Deficiencies of micronutrients like vitamin A, iron and zinc are widely prevalent among populations living in developing countries. Besides their severe deficiencies, subclinical deficiencies are known to impair biological functions in the host, immune function being one of them. The effects of these micronutrients on various immune mechanisms are briefly reviewed in this article.
Importance of folate in human nutrition
Authors: Krishnaswamy Kamala , Nair K. Madhavan
Published: October 2009

From a public health perspective, some of the new insights into folic acid nutrition are of significance. Folate intake recommendations vary under different conditions. Intake of 350 μg is required to maintain plasma homocysteine levels, 650 μg for those with elevated plasma homocysteine, about 400 μg for women planning to become pregnant and 4000 μg for those with history of neural tube defect affected pregnancy. This raises the question whether the folate intake is adequate for the general population, particularly in the vulnerable groups or whether there is a need for scientists to take a fresh view of the requirements, recommended dietary intakes, and consider intervention measures which will have impact on the folate nutritional status. The recommendations should provide a margin of safety to allow for decreased intake, increased requirements, individual variability and bioavailability of natural food folates. The folate intake and nutriture in relation to India and other developing countries needs careful consideration to reduce anemia, neural tube defects and possibly impact on the high incidence of cardiovascular diseases.
Zinc and childhood infectious disease morbidity and mortality
Authors: Black Robert E. , Sazawal Sunil
Published: October 2009

Zinc is an essential mineral and deficiency results in abnormal immune function and higher rates of infectious diseases. Randomized controlled trials of zinc supplementation have been conducted in children in developing countries to determine effects on infectious disease morbidity and mortality. Zinc-supplemented children have been found to have lower rates of diarrhea, pneumonia and malaria in comparison with children not given zinc. Zinc used as an adjunct to fluid and dietary management of acute and persistent diarrhea has been found to reduce diarrheal duration and severity. Preliminary evidence suggests that zinc supplementation in children in poor developing country settings may also reduce infant mortality, but larger trials are needed to address this important issue. Preventive and therapeutic interventions should be implemented in developing countries where zinc deficiency is likely to be prevalent.
Micronutrients as adjunct therapy of acute illness in children: impact on the episode outcome and policy implications of current findings
Authors: Mahalanabis Dilip , Bhan Maharaj K.
Published: October 2009

Role of micronutrients namely vitamin A, zinc and folate, as adjunct therapy of illness episodes in children in developing countries have been discussed in the light of health policy. Apart from a selective review, attempts have been made to statistically combine results of several studies to address policy issues. In children, vitamin A supplementation during illness has (a) a profound effect in reducing mortality in measles, (b) possibly a significant effect in reducing persistent diarrhea episodes in children with acute diarrhea, and (c) no benefit in pneumonia.

Use of large dose vitamin A is recommended during measles episodes but not in non-measles pneumonia. Its use in acute diarrhea is debatable but recommended in persistent diarrhea and in severe malnutrition as a component of a micronutrient mixture. Large dose vitamin A supplementation should be used with caution in young infants as there are unresolved concerns about its safety particularly, bulging fontanelle observed in infants when co-administered at immunization. In children, zinc supplementation during illness, (a) had a marked effect in reducing prolonged episodes and a modest effect on episode duration in acute diarrhea, (b) resulted in reduced rate of treatment failure and death in persistent diarrhea, (c) had no effect in measles and non-measles pneumonia, and (d) probably had a detrimental effect of increasing death rate when a large dose was used in severely malnourished children. The desirability of routine zinc supplementation therapy of undernourished children with acute diarrhea should be assessed further. Concerning policy, zinc supplementation as a component of a micronutrient mixture is recommended in the rehabilitation of severely malnourished children and in persistent diarrhea. However, recommendation for its routine use in all cases of acute diarrhea in children needs additional studies on effectiveness, cost, operations and safety. In two randomized controlled trials folate has been evaluated in acute and persistent diarrhea and found to have no beneficial effect. Folate is not recommended as adjunct therapy of diarrhea. Role of folate in preventing severe disease and/or death deserves further evaluation.
Quantitative measurement of aging using image texture entropy
Authors: Shamir Lior , Wolkow Catherine A. , Goldberg Ilya G.
Published: October 2009

Motivation: A key element in understanding the aging of Caenorhabditis elegans is objective quantification of the morphological differences between younger and older animals. Here we propose to use the image texture entropy as an objective measurement that reflects the structural deterioration of the C.elegans muscle tissues during aging.

Results: The texture entropy and directionality of the muscle microscopy images were measured using 50 animals on Days 0, 2, 4, 6, 8, 10 and 12 of adulthood. Results show that the entropy of the C.elegans pharynx tissues increases as the animal ages, but a sharper increase was measured between Days 2 and 4, and between Days 8 and 10. These results are in agreement with gene expression findings, and support the contention that the process of C.elegans aging has several distinct stages. This can indicate that C.elegans aging is driven by developmental pathways, rather than stochastic accumulation of damage.

Availability: The image data are freely available on the Internet at http://ome.grc.nia.nih.gov/iicbu2008/celegans, and the Haralick and Tamura texture analysis source code can be downloaded at http://ome.grc.nia.nih.gov/wnd-charm.

Contact:  shamirl@mail.nih.gov
CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score
Authors: Hamada Michiaki , Sato Kengo , Kiryu Hisanori , Mituyama Toutai , Asai Kiyoshi
Published: October 2009

Motivation: The importance of accurate and fast predictions of multiple alignments for RNA sequences has increased due to recent findings about functional non-coding RNAs. Recent studies suggest that maximizing the expected accuracy of predictions will be useful for many problems in bioinformatics.

Results: We designed a novel estimator for multiple alignments of structured RNAs, based on maximizing the expected accuracy of predictions. First, we define the maximum expected accuracy (MEA) estimator for pairwise alignment of RNA sequences. This maximizes the expected sum-of-pairs score (SPS) of a predicted alignment under a probability distribution of alignments given by marginalizing the Sankoff model. Then, by approximating the MEA estimator, we obtain an estimator whose time complexity is O(L3+c2dL2) where L is the length of input sequences and both c and d are constants independent of L. The proposed estimator can handle uncertainty of secondary structures and alignments that are obstacles in Bioinformatics because it considers all the secondary structures and all the pairwise alignments as input sequences. Moreover, we integrate the probabilistic consistency transformation (PCT) on alignments into the proposed estimator. Computational experiments using six benchmark datasets indicate that the proposed method achieved a favorable SPS and was the fastest of many state-of-the-art tools for multiple alignments of structured RNAs.

Availability: The software called CentroidAlign, which is an implementation of the algorithm in this article, is freely available on our website: http://www.ncrna.org/software/centroidalign/.

Contact:  hamada-michiaki@aist.go.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Excoecarianin, Isolated fromPhyllanthus urinariaLinnea, Inhibits Herpes Simplex Virus Type 2 Infection through Inactivation of Viral Particles
Authors: Cheng Hua-Yew , Yang Chien-Min , Lin Ta-Chen , Lin Liang-Tzung , Chiang Lien-Chai , Lin Chun-Ching
Published: October 2009

Phyllanthus urinariaLinnea (Euphorbiaceae) is one of the traditional medicinal plants widely used by oriental people to treat various diseases. We have previously demonstrated that the acetone extract ofP. urinariainhibits herpes simplex virus type 2 (HSV‐2) but not HSV‐1 infection. In a continuing effort to clarify the antiviral mechanisms ofP. urinaria, we isolated the pure compound excoecarianin from the whole plant ofP. urinariathrough acetone extraction, and investigated its anti‐HSV‐1 and HSV‐2 activities. Our results indicated that excoecarianin protected Vero cells from HSV‐2 but not HSV‐1 infection, and its 50% inhibitory concentration (IC50) was 1.4 ± 0.1 μM. The antiviral effective concentration of excoecarianin did not affect the viability or the morphology of Vero cells. Although excoecarianin inhibited HSV‐2 infection, the inhibitory effect, however, was most prominent when excoecarianin was concurrently added with the virus. Pretreatment of Vero cells with excoecarianin with removal of the drug prior to infection did not yield any antiviral effects, and the same observation was made for post viral entry treatment. Subsequent studies revealed that excoecarianin inactivated HSV‐2 virus particles to prevent viral infection. A synergistic antiviral effect against HSV‐2 was also observed when Vero cells were treated with a combination of acyclovir (ACV) and excoecarianin. These results suggested that excoecarianin merits to be further explored as an entry inhibitor against HSV‐2 and could potentially be investigated for combinatorial drug treatment with nucleoside analogues such as ACV in therapeutic management of HSV‐2 infection.
Transcriptional Changes and Oxidative Stress Associated with the Synergistic Interaction BetweenPotato virus XandPotato virus Yand Their Relationship with Symptom Expression
Authors: García-Marcos Alberto , Pacheco Remedios , Martiáñez Justo , González-Jara Pablo , Díaz-Ruíz José Ramón , Tenllado Francisco
Published: October 2009

Many virus diseases of economic importance to agriculture result from mixtures of different pathogens invading the host at a given time. This contrasts with the relatively scarce studies available on the molecular events associated with virus–host interactions in mixed infections. Compared with single infections, co-infection of Nicotiana benthamiana with Potato virus X (PVX) and Potato virus Y (PVY) resulted in increased systemic symptoms (synergism) that led to necrosis of the newly emerging leaves and death of the plant. A comparative transcriptional analysis was undertaken to identify quantitative and qualitative differences in gene expression during this synergistic infection and correlate these changes with the severe symptoms it caused. Global transcription profiles of doubly infected leaves were compared with those from singly infected leaves using gene ontology enrichment analysis and metabolic pathway annotator software. Functional gene categories altered by the double infection comprise suites of genes regulated coordinately, which are associated with chloroplast functions (downregulated), protein synthesis and degradation (upregulated), carbohydrate metabolism (upregulated), and response to biotic stimulus and stress (upregulated). The expressions of reactive oxygen species–generating enzymes as well as several mitogen-activated protein kinases were also significantly induced. Accordingly, synergistic infection induced a severe oxidative stress in N. benthamiana leaves, as judged by increases in lipid peroxidation and by the generation of superoxide radicals in chloroplasts, which correlated with the misregulation of antioxidative genes in microarray data. Interestingly, expression of genes encoding oxylipin biosynthesis was uniquely upregulated by the synergistic infection. Virus-induced gene silencing of α-dioxygenase1 delayed cell death during PVX–PVY infection.
Detection, Distribution, and Genetic Variability of ‘Candidatus Liberibacter’ Species Associated with Zebra Complex Disease of Potato in North America
Authors: Wen A. , Mallik I. , Alvarado V. Y. , Pasche J. S. , Wang X. , Li W. , Levy L. , Lin H. , Scholthof H. B. , Mirkov T. E. , Rush C. M. , Gudmestad N. C.
Published: October 2009

The specificity and sensitivity of polymerase chain reaction (PCR) primers developed for ‘Candidatus Liberibacter solanacearum’ and ‘Candidatus Liberibacter psyllaurous’ were evaluated in conventional and real-time PCR assays. All PCR primers were specific for ‘Ca. L. psyllaurous’ and ‘Ca. L. solanacearum’ insomuch as they did not detect other prokaryotic plant pathogens that affect potato except for the putative pathogens associated with psyllid-yellows and haywire. Conventional PCR assays were capable of detecting 0.19 to 1.56 ng of total DNA per reaction, and real-time PCR was found capable of detecting 1.56 to 6.25 ng of total DNA per reaction, depending on the specific PCR primer set used. ‘Ca. Liberibacter’ species associated with zebra complex disease (ZC) was confirmed in plants affected by this disease throughout Texas from 2005 to 2008, in seed tubers produced in Wyoming in 2007, and in Colorado, Kansas, Nebraska, and Mexico in 2008. A multiplex PCR assay using ‘Ca. L. solanacearum’–specific primers and primers specific for the β-tubulin DNA regions from potato was developed, providing possible utility of the multiplex assay for ‘Ca. Liberibacter’ detection in different solanaceous plant species. Preliminary studies suggest silverleaf nightshade (Solanum elaeagnifolium), wolfberry (Lycium barbarum), black nightshade (S. ptychanthum), and jalapeno pepper (Capsicum annuum) as additional solanaceous hosts for the ZC-associated bacterium. The ‘Ca. Liberibacter’ species detected in all samples divided into two clusters sharing similarity of 99.8% in their partial 16S rRNA gene sequences and 99.3% in their partial intergenic spacer region (ISR)-23S rRNA gene sequences. Genetic variation in the 16S rDNA region consistently matched that of the ISR-23S rDNA region. In this partial 16S-ISR-23S rDNA region, there was a total of eight single nucleotide polymorphisms among ‘Ca. L. psyllaurous’ and ‘Ca. L. solanacearum’ “strains” investigated in this study. ‘Ca. L. solanacearum’ and ‘Ca. L. psyllaurous’ were shown to be very closely related bacteria, if not the same, by successful amplification using a combination of forward primer of ‘Ca. L. solanacearum’ and reverse primer of ‘Ca. L. psyllaurous’ in ZC-affected potato samples. This finding clarifies the current taxonomic status of ‘Ca. L. solanacearum’ and ‘Ca. L. psyllaurous’. The detection of ‘Ca. L. solanacearum’ from haywire-symptomatic potato samples demonstrates that this bacterium might also be associated with this disease.
Leaf Scorch of Purple-Leafed Plum and Sweetgum Dieback: Two New Diseases in Southern California Caused by Xylella fastidiosa Strains with Different Host Ranges
Authors: Hernandez-Martinez R. , Cooksey D. A. , Wong F. P.
Published: October 2009

Sweetgum dieback and leaf scorch of purple-leafed plum are two new diseases of southern California landscape ornamentals. Samplings were conducted in 2003 and 2004 and 28 of 105 sweetgum (Liquidambar styraciflua) and 38 of 62 purple-leafed plum (Prunus cerasifera) plants tested positive for Xylella fastidiosa by enzyme linked immunosorbent assay. In all, 3 strains of X. fastidiosa were isolated from sweetgum and 13 from purple-leafed plum. All sweetgum strains and some purple-leafed plum strains grew on PW but not PD3 media. Strain PC045 from purple-leafed plum and strain LS022 from sweetgum were inoculated into their original hosts in addition to almond, oleander, and grapevine plants. Sweetgum plants also were inoculated with strains causing Pierce's disease, almond leaf scorch, and oleander leaf scorch. Strain PC045 caused symptoms in purple-leafed plum and almond plants within 6 months, and the pathogen was recovered from 93 and 100% of inoculated plants, respectively. Inoculation of grapevine and oleander plants with PC045 did not result in disease or recovery of the pathogen. In all, 5 of 25 sweetgum plants inoculated with LS022 showed symptoms after 9 months, and the pathogen was recovered from 3 of these plants. Inoculation of grapevine, oleander, and almond with LS022 resulted in no disease or recovery of the pathogen from the plants. A strain of Pierce's disease, a strain of oleander leaf scorch, and two strains from almond did not cause disease in sweetgum. These results confirm the role of X. fastidiosa strains as pathogens of purple-leafed plum and sweetgum, and that strains from sweetgum are unique in their host range.
Effect of Brown Rust on Yield of Sugarcane in Louisiana
Authors: Hoy J. W. , Hollier C. A.
Published: October 2009

Brown rust, caused by Puccinia melanocephala, can cause severe epidemics in susceptible sugarcane cultivars during spring and early summer in Louisiana. The effect of the disease on yield was evaluated in field experiments conducted during three growing seasons. A mixture of three fungicides—azoxystrobin, propiconazole, and tebuconazole—applied biweekly during the spring epidemic period kept brown rust severity low (<5%), and plants protected by fungicide applications throughout the epidemic provided an estimate of attainable yield for comparison with plants naturally infected with rust. A combined analysis over three seasons estimated brown rust caused reductions of 16 and 14% in cane tonnage and total amount of sucrose produced, respectively, in cv. LCP 85-384. The greatest reduction in total sucrose yield of 22% resulted from the epidemic of longest duration, and stalk weight was negatively correlated with rust severity. Comparisons of the yields obtained from plots in which brown rust was controlled early versus late in the epidemic suggested that the impact of the disease is greatest from the middle to late epidemic period when stem elongation has begun.
Effect of Cultural Management Practices on the Severity of False Smut and Kernel Smut of Rice
Authors: Brooks Steven A. , Anders Merle M. , Yeater Kathleen M.
Published: October 2009

False smut (Ustilaginoidea virens) and kernel smut (Neovossia horrida) are diseases of rice (Oryza sativa) that reduce both grain yield and quality. False smut is an emerging disease worldwide that is rapidly gaining in importance, whereas kernel smut has historically been a chronic minor disease with sporadic outbreaks that cause considerable losses. Highly effective disease control was obtained for susceptible cultivars by employing conservation tillage (69% reduction in false smut), continuous rice cropping (88% reduction in false smut), and moderate nitrogen fertility rates (34 and 60% reductions in false smut and kernel smut, respectively). Combining these treatments nearly eliminated smuts from cultivars that were fully susceptible under conventional cultivation practices. Furthermore, using a nursery designed to promote smut diseases, two rice hybrids were identified that possessed kernel smut resistance under the most favorable disease conditions. The genetic basis of the resistance is unknown. However, the utility for disease control is great because hybrids occupy significant portions of production rice acreage.
First Report of Bacterial Head Rot of Broccoli Caused by Pseudomonas fluorescens in China
Authors: Li B. , Wang G. L. , Wu Z. Y. , Qiu W. , Tang Q. M. , Xie G. L.
Published: October 2009

During warm and humid periods in the winters from 2005 to 2008, head rot symptoms on broccoli (cv. Sijilv) (Brassica oleracea L. var italica Planch) were observed in commercial fields in Ningbo, Zhejiang Province, China. In agreement with the report of Cui and Harling (1), water-soaked lesions developed on the buds and then progressed into a brown-black soft rot. Longitudinal sections of the symptomatic inflorescences showed brown discoloration and rotting of the internal tissues. Broccoli production is hampered by the disease, with disease incidence ranging from 65 to 81%. Bacteria were isolated by streaking on nutrient agar (3) and individual colonies formed after 2 to 3 days of incubation at 28°C. Fifteen of thirty isolates induced hypersensitive reactions (HR) on tobacco leaves (Nicotiana tabacum cv. Samsun) within 48 h. All the HR-positive strains were fluorescent on King's medium B and the colonies were smooth, convex, entire, and round. Classical bacteriological tests indicated that the fluorescent strains were gram negative, obligate aerobes, arginine dihydrolase positive, and oxidase positive. Also, the fluorescent strains were positive for the production of levan from sucrose. Five representative strains were further characterized by the Biolog Microbial Identification System, version 4.2 (Biolog Inc., Hayward, CA) and gas chromatography of fatty acid methyl esters (FAME) using the Microbial Identification System (MIDI Inc., Newark, DE) with the aerobic bacterial library (TSBA50). The five strains were identified as Pseudomonas fluorescens with Biolog and FAME similarity indexes of 0.61 to 0.68 and 0.52 to 0.58, respectively. The 16S rRNA gene sequence of broccoli strain PFB-01 (GenBank Accession No. GQ352649) was determined according to Li et al. (2). A subsequent GenBank search showed that this sequence had 98% nucleotide identity with the type strain of P. fluorescens (ATCC 17386T, GenBank Accession No. AF094726). Koch's postulates were completed by the inoculation of broccoli heads (cv. Sijilv) with cell suspensions (107 CFU/ml) of the above five strains by spraying on the surface of subcorymbs. Each treatment had five replicates. All strains induced head rot symptoms similar to those observed in natural infections. No symptoms were noted on the control plants inoculated with sterile water. Bacteria were successfully reisolated from symptomatic heads and confirmed by the cellular fatty acid composition. To our knowledge, this is the first report in China that P. fluorescens is the causal pathogen of bacterial head rot of broccoli.

References: (1) X. Cui and R. Harling. Phytopathology 96:408, 2006. (2) B. Li et al. J. Phytopathol. 154:711, 2006. (3) N. W. Schaad et al. Laboratory Guide for Identification of Plant Pathogenic Bacteria. 3rd ed. The American Phytopathological Society. St. Paul, MN, 2001.
Invasive meningococcal disease in Malta: an epidemiological overview, 1994–2007
Authors: Muscat Mark , Spiteri Gianfranco , Calleja Neville , Haider Julie , Gray Stephen J. , Melillo Jackie Maistre , Mamo Julian , Cuschieri Paul
Published: October 2009

Since 1996, Malta has experienced an upsurge of invasive meningococcal disease (IMD) following an almost 30 year period with a negligible number of annually reported cases. We reviewed the 233 IMD cases notified during a 14 year period (1994–2007), and analysed epidemiological and laboratory surveillance data. The crude incidence per 100 000 inhabitants peaked in 2000 at 8.1 [95 % confidence interval (CI) 5.7–11.6] and again in 2006 at 8.9 (95 % CI 6.4–12.4), thereby placing Malta amongst the countries with the highest incidence of the disease in Europe. Of the total cases, 137 (59 %) were confirmed and 30 (13 %) were classified as probable. However, 66 cases (28 %) had no laboratory evidence of the disease and were classified as possible. Information on the serogroup was available for 114 cases. Serogroup B formed the largest proportion (76 %, n=87) followed by serogroup C (16 %, n=18). B : 4 : P1.19,15 strains (n=46) predominated throughout the study period since their first identification in 1998. With 28 deaths attributed to IMD, the overall case fatality rate was 12 %. Apart from stressing the importance of maintaining high vigilance for IMD, our findings underscore the importance of enhancing laboratory surveillance of the disease, including characterization of the meningococci. Until vaccines against a broad range of serogroup B meningococci become available for universal use, the main methods of control remain the early treatment of cases and the prevention of secondary cases.
Clonal dissemination of human isolates of Streptococcus suis serotype 14 in Thailand
Authors: Kerdsin Anusak , Oishi Kazunori , Sripakdee Saowalak , Boonkerd Nitsara , Polwichai Pitimol , Nakamura Shota , Uchida Ryuichi , Sawanpanyalert Pathom , Dejsirilert Surang
Published: October 2009

Most cases of Streptococcus suis infection in humans are caused by serotype 2 strains, and only a few cases caused by other serotypes have been reported. Among 177 human isolates of S. suis in Thailand, 12 (6.8 %) were identified as being of serotype 14, and an occurrence of sporadic S. suis serotype 14 infection was noted during 2006–2008, particularly in northern Thailand. Clinical presentations of the 12 patients (median age 62.9 years) included meningitis (58.3 %), septic arthritis (25 %) and sepsis (16.7 %). These clinical features were similar to those previously reported for S. suis infections, except that there were no fatal cases. All of the 12 serotype 14 strains belonged to the multilocus sequence types (ST) 105 (n=11) and the novel ST127 (n=1). Molecular typing by PFGE revealed four different pulsotypes, including an identical pattern for nine ST105 strains and three closely related patterns for two ST105 strains and one ST127 strain. Our PFGE data suggested clonal dissemination of ST105 strains in Thailand. Because serotype 14 is becoming a more common cause of S. suis infections in humans, diagnostic tests for serotype 14 should be performed in South-East Asian countries.
Smallpox vaccines induce antibodies to the immunomodulatory, secreted vaccinia virus complement control protein
Authors: Adamo Joan E. , Meseda Clement A. , Weir Jerry P. , Merchlinsky Michael J.
Published: October 2009

Vaccination with Dryvax elicits a broad humoral response against many viral proteins. Human vaccinia immune globulin was used to screen the secreted proteins from cells infected with Dryvax or the candidate smallpox vaccine LC16m8 to determine whether the protective humoral response included antibodies against secreted viral proteins. Many proteins were detected, with the primary band corresponding to a band of 28 or 30 kDa in cells infected with Dryvax or LC16m8, respectively. This was identified as the vaccinia virus complement protein (VCP), which migrated more slowly in LC16m8-infected cells due to post-translational glycosylation. Vaccinia virus deleted in VCP, vVCPko, protected mice from a lethal intranasal challenge of vaccinia Western Reserve strain. Mice vaccinated with purified VCP demonstrated a strong humoral response, but were not protected against a moderate lethal challenge of vaccinia virus, suggesting that the humoral response against VCP is not critical for protection.
Isolation and genomic characterization of the first Norway rat (Rattus norvegicus) papillomavirus and its phylogenetic position within Pipapillomavirus, primarily infecting rodents
Authors: Schulz Eric , Gottschling Marc , Wibbelt Gudrun , Stockfleth Eggert , Nindl Ingo
Published: October 2009

A series of papillomavirus (PV) types have been isolated from different rodent species, and most of them belong to the genus Pipapillomavirus. We isolated and sequenced the complete genome of a novel PV type (designated RnPV) from the oral cavity of the Norway rat (Rattus norvegicus), as well as an L1 gene fragment from hair-follicle cells of the European beaver (Castor fiber). As inferred from amino acid sequence data, RnPV clustered within the β+γ+π+Ξ-PV supertaxon as a member of the genus Pipapillomavirus. The closest relatives of RnPV were McPV-2 and MmPV, and time estimates indicated that the genus Pipapillomavirus originated in the late Cenozoic era. The close relationship of RnPV to other murid PV types supports the hypothesis of co-divergence between members of the genus Pipapillomavirus and their hosts. However, the derived Neogene origin of the genus Pipapillomavirus is much younger than has been considered for the Rodentia as the primary hosts, indicating that alternative interpretations of the phylogenetic trees should be conceived.
Angiotensin-converting enzyme 2 (ACE2) from raccoon dog can serve as an efficient receptor for the spike protein of severe acute respiratory syndrome coronavirus
Authors: Xu Lili , Zhang Yanfang , Liu Yun , Chen Zhiwei , Deng Hongkui , Ma Zhongbin , Wang Hualin , Hu Zhihong , Deng Fei
Published: October 2009

Raccoon dog is one of the suspected intermediate hosts of severe acute respiratory syndrome coronavirus (SARS-CoV). In this study, the angiotensin-converting enzyme 2 (ACE2) gene of raccoon dog (rdACE2) was cloned and sequenced. The amino acid sequence of rdACE2 has identities of 99.3, 89.2, 83.9 and 80.4 % to ACE2 proteins from dog, masked palm civet (pcACE2), human (huACE2) and bat, respectively. There are six amino acid changes in rdACE2 compared with huACE2, and four changes compared with pcACE2, within the 18 residues of ACE2 known to make direct contact with the SARS-CoV S protein. A HeLa cell line stably expressing rdACE2 was established; Western blot analyses and an enzyme-activity assay indicated that the cell line expressed ACE2 at a similar level to two previously established cell lines that express ACE2 from human and masked palm civet, respectively. Human immunodeficiency virus-backboned pseudoviruses expressing spike proteins derived from human SARS-CoV or SARS-CoV-like viruses of masked palm civets and raccoon dogs were tested for their entry efficiency into these cell lines. The results showed that rdACE2 is a more efficient receptor for human SARS-CoV, but not for SARS-CoV-like viruses of masked palm civets and raccoon dogs, than huACE2 or pcACE2. This study provides useful data to elucidate the role of raccoon dog in SARS outbreaks.
Interferon priming enables cells to partially overturn the SARS coronavirus-induced block in innate immune activation
Authors: Kuri Thomas , Zhang Xiaonan , Habjan Matthias , Martínez-Sobrido Luis , García-Sastre Adolfo , Yuan Zhenghong , Weber Friedemann
Published: October 2009

SARS coronavirus (SARS-CoV) is known to efficiently suppress the induction of antiviral type I interferons (IFN-α/β) in non-lymphatic cells through inhibition of the transcription factor IRF-3. Plasmacytoid dendritic cells, in contrast, respond to infection with production of high levels of IFNs. Here, we show that pretreatment of non-lymphatic cells with small amounts of IFN-α (IFN priming) partially overturns the block in IFN induction imposed by SARS-CoV. IFN priming combined with SARS-CoV infection substantially induced genes for IFN induction, IFN signalling, antiviral effector proteins, ubiquitination and ISGylation, antigen presentation and other cytokines and chemokines, whereas each individual treatment had no major effect. Curiously, however, despite this typical IFN response, neither IRF-3 nor IRF-7 was transported to the nucleus as a sign of activation. Taken together, our results suggest that (i) IFN, as it is produced by plasmacytoid dendritic cells, could enable tissue cells to launch a host response to SARS-CoV, (ii) IRF-3 and IRF-7 may be active at subdetectable levels, and (iii) SARS-CoV does not activate IRF-7.
Hepatitis B virus and hepatitis delta virus genotypes in outbreaks of fulminant hepatitis (Labrea black fever) in the western Brazilian Amazon region
Authors: Gomes-Gouvêa M. S. , Soares M. C. P. , Bensabath G. , de Carvalho-Mello I. M. V. G. , Brito E. M. F. , Souza O. S. C. , Queiroz A. T. L. , Carrilho F. J. , Pinho J. R. R.
Published: October 2009

The genotypes of hepatitis B (HBV) and delta (HDV) viruses circulating among fulminant hepatitis cases from the western Amazon Basin of Brazil were characterized in this study. HBV and HDV isolates were obtained from liver samples from 14 patients who developed fulminant hepatitis and died during 1978–1989. HBV DNA and HDV RNA were detected in all samples. Phylogenetic analyses of HDV sequences showed that they all clustered with previously characterized sequences of HDV genotype 3 (HDV-3). HBV genotypes F, A and D were found in 50.0, 28.6 and 21.4 % of cases, respectively. These results confirm the predominance of HDV-3 in South America and its association with the severe form of hepatitis, and the finding of the co-infection of HDV-3 with different genotypes of HBV suggests that the association between HDV-3 and HBV-F is not necessarily causally related to a more severe clinical course of infection.
Virulence of pigeon paramyxovirus type 1 does not always correlate with the cleavability of its fusion protein
Authors: Dortmans J. C. F. M. , Koch G. , Rottier P. J. M. , Peeters B. P. H.
Published: October 2009

Some pigeon paramyxovirus type 1 (PPMV-1) strains exhibit low virulence in chickens, despite their fusion (F) protein's multi-basic cleavage site. To elucidate the molecular basis of the low pathogenicity of these strains, we constructed an infectious full-length cDNA clone of PPMV-1 strain AV324. This strain is non-virulent for chickens, although its F protein contains the typical virulence motif 112RRKKRF117. By using reverse genetics, we exchanged the F genes of AV324 and a virulent Newcastle disease virus (NDV) strain (Herts) and evaluated the recovered chimeric viruses for their pathogenicity in 1-day-old chickens and in embryonated eggs. Our results show that the F protein of AV324, and probably those of similar PPMV-1 strains, are functionally not different from those of virulent NDV strains and that the difference in pathogenicity must be determined by other factors.
Influenza A virus M1 blocks the classical complement pathway through interacting with C1qA
Authors: Zhang Junjie , Li Gang , Liu Xiaoling , Wang Zengfu , Liu Wenjun , Ye Xin
Published: October 2009

The matrix (M1) protein of influenza A virus is a conserved multifunctional protein that plays essential roles in regulating the viral life cycle. This study demonstrated that M1 is able to interact with complement C1qA and plays an important inhibitory function in the classical complement pathway. The N-terminal domain of M1 protein was required for its binding to the globular region of C1qA. As a consequence, M1 blocked the interaction between C1qA and heat-aggregated IgGin vitroand inhibited haemolysis. It was shown that M1 protein prevented the complement-mediated neutralization of influenza virusin vitro. In addition, studies on mice indicated that the administration of M1 could promote a higher virus propagation rate in lung and shortened survival of mice infected with the virus. Taken together, these results suggest strongly that the M1 protein plays a critical role in protecting influenza virus from the host innate immune system.