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https://www.readbyqxmd.com/read/28213872/capulavirus-and-grablovirus-two-new-genera-in-the-family-geminiviridae
#1
Arvind Varsani, Philippe Roumagnac, Marc Fuchs, Jesús Navas-Castillo, Enrique Moriones, Ali Idris, Rob W Briddon, Rafael Rivera-Bustamante, F Murilo Zerbini, Darren P Martin
Geminiviruses are plant-infecting single-stranded DNA viruses that occur in most parts of the world. Currently, there are seven genera within the family Geminiviridae (Becurtovirus, Begomovirus, Curtovirus, Eragrovirus, Mastrevirus, Topocuvirus and Turncurtovirus). The rate of discovery of new geminiviruses has increased significantly over the last decade as a result of new molecular tools and approaches (rolling-circle amplification and deep sequencing) that allow for high-throughput workflows. Here, we report the establishment of two new genera: Capulavirus, with four new species (Alfalfa leaf curl virus, Euphorbia caput-medusae latent virus, French bean severe leaf curl virus and Plantago lanceolata latent virus), and Grablovirus, with one new species (Grapevine red blotch virus)...
February 17, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28198678/gaap-genome-organization-framework-assisted-assembly-pipeline-for-prokaryotic-genomes
#2
Lina Yuan, Yang Yu, Yanmin Zhu, Yulai Li, Changqing Li, Rujiao Li, Qin Ma, Gilman Kit-Hang Siu, Jun Yu, Taijiao Jiang, Jingfa Xiao, Yu Kang
BACKGROUND: Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. RESULTS: Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28160447/-medusa-head-cells-starfish-cells-and-interconnecting-long-cytoplasmic-processes-as-diagnostic-cytologic-clues-for-follicular-dendritic-cell-sarcoma-in-fine-needle-aspiration-samples
#3
Agata Czapla, Reeba A Omman, Moon Woo Nam, Swati Mehrotra, Stefan E Pambuccian
No abstract text is available yet for this article.
February 3, 2017: Diagnostic Cytopathology
https://www.readbyqxmd.com/read/28155633/multi-car-a-tool-of-contig-scaffolding-using-multiple-references
#4
Kun-Tze Chen, Cheih-Jung Chen, Hsin-Ting Shen, Chia-Liang Liu, Shang-Hao Huang, Chin Lung Lu
BACKGROUND: A draft genome assembled by current next-generation sequencing techniques from short reads is just a collection of contigs, whose relative positions and orientations along the genome being sequenced are unknown. To further obtain its complete sequence, a contig scaffolding process is usually applied to order and orient the contigs in the draft genome. Although several single reference-based scaffolding tools have been proposed, they may produce erroneous scaffolds if there are rearrangements between the target and reference genomes or their phylogenetic relationship is distant...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28052087/high-abundance-of-the-epibenthic-trachymedusa-ptychogastria-polaris-allman-1878-hydrozoa-trachylina-in-subpolar-fjords-along-the-west-antarctic-peninsula
#5
Laura J Grange, Craig R Smith, Dhugal J Lindsay, Bastian Bentlage, Marsh J Youngbluth
Medusae can be conspicuous and abundant members of seafloor communities in deep-sea benthic boundary layers. The epibenthic trachymedusa, Ptychogastria polaris Allman, 1878 (Hydrozoa: Trachylina: Ptychogastriidae) occurs in the cold, high latitude systems of both the northern and southern hemispheres, with a circumpolar distribution in Arctic and sub-Arctic areas, and disjunct reports of a few individuals from Antarctica. In January-February 2010, during benthic megafaunal photosurveys in three subpolar fjords along the West Antarctic Peninsula (Andvord, Flandres and Barilari Bays), P...
2017: PloS One
https://www.readbyqxmd.com/read/28000727/evidence-of-cnidarians-sensitivity-to-sound-after-exposure-to-low-frequency-noise-underwater-sources
#6
Marta Solé, Marc Lenoir, José Manuel Fontuño, Mercè Durfort, Mike van der Schaar, Michel André
Jellyfishes represent a group of species that play an important role in oceans, particularly as a food source for different taxa and as a predator of fish larvae and planktonic prey. The massive introduction of artificial sound sources in the oceans has become a concern to science and society. While we are only beginning to understand that non-hearing specialists like cephalopods can be affected by anthropogenic noises and regulation is underway to measure European water noise levels, we still don't know yet if the impact of sound may be extended to other lower level taxa of the food web...
December 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27994268/automated-assessment-of-joint-synovitis-activity-from-medical-ultrasound-and-power-doppler-examinations-using-image-processing-and-machine-learning-methods
#7
Rafal Cupek, Adam Ziębiński
OBJECTIVES: Rheumatoid arthritis is the most common rheumatic disease with arthritis, and causes substantial functional disability in approximately 50% patients after 10 years. Accurate measurement of the disease activity is crucial to provide an adequate treatment and care to the patients. The aim of this study is focused on a computer aided diagnostic system that supports an assessment of synovitis severity. MATERIAL AND METHODS: This paper focus on a computer aided diagnostic system that was developed within joint Polish-Norwegian research project related to the automated assessment of the severity of synovitis...
2016: Reumatologia
https://www.readbyqxmd.com/read/27992167/the-eye-of-the-medusa-xrf-imaging-reveals-unknown-traces-of-antique-polychromy
#8
Matthias Alfeld, Maud Mulliez, Philippe Martinez, Kevin Cain, Philippe Jockey, Philippe Walter
The colorful decoration of statues and buildings in antique times is commonly described by the term antique polychromy. It is well-known among scholars but less so to the general public, and its exact form is the subject of research. In this paper we discuss results obtained from the frieze of the Siphnian Treasury in the Sanctuary of Delphi (Greece). We will present the first application of a mobile instrument for macro-XRF imaging for the in situ investigation of antique polychromy and show that it allows one to identify significant traces not visible to the naked eye and not detectable by XRF spot measurements or any other mobile, noninvasive method...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/27890264/selective-suppression-of-in-situ-proliferation-of-scyphozoan-polyps-by-biofouling
#9
Song Feng, Shi-Wei Wang, Guang-Tao Zhang, Song Sun, Fang Zhang
An increase in marine artificial constructions has been proposed as a major cause of jellyfish blooms, because these constructions provide additional substrates for organisms at the benthic stage (polyps), which proliferate asexually and release a large amount of free-swimming medusae. These hard surfaces are normally covered by fouling communities, the components of which have the potential to impede the proliferation of polyps. In this study, we report an in situ experiment of polyp survival of four large scyphozoan species found in East Asian marginal seas that were exposed to biofouling, a universal phenomenon occurring on marine artificial constructions...
January 30, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/27880678/evidence-for-an-alternative-mechanism-of-toxin-production-in-the-box-jellyfish-alatina-alata
#10
Cheryl Lewis Ames, Jason Macrander
Cubozoans (box jellyfish) have a reputation as the most venomous animals on the planet. Herein, we provide a review of cubozoan prey capture and digestion informed by the scientific literature. Like all cnidarians, box jellyfish envenomation originates from structures secreted within nematocyte post-Golgi vesicles called nematocysts. When tentacles come in contact with prey or would-be predators, a cocktail of toxins is rapidly deployed from nematocysts via a long spiny tubule that serves to immobilize the target organism...
November 2016: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/27858592/ultrasound-guided-access-into-the-abdomen-in-the-setting-of-portal-hypertension-a-novel-technique
#11
Cory N Criss, Matthew W Ralls, Marcus D Jarboe
As the field of minimally invasive surgery rapidly evolves, there is an opportunity to adopt innovative techniques to accommodate a variety of patient populations. In patients with portal hypertension, a major risk factor upon entry into the abdomen is injury to large, engorged paraumbilical vessels in the anterior abdominal wall. Major blood loss often results from just entering the abdomen. Here, we describe a patient with caput medusae secondary to portal hypertension presenting for laparoscopic repair of a ventral hernia...
November 18, 2016: Journal of Laparoendoscopic & Advanced Surgical Techniques. Part A
https://www.readbyqxmd.com/read/27845203/complete-mitochondrial-genome-and-evolutionary-analysis-of-turritopsis-dohrnii-the-immortal-jellyfish-with-a-reversible-life-cycle
#12
A A Lisenkova, A P Grigorenko, T V Tyazhelova, T V Andreeva, F E Gusev, A D Manakhov, A Yu Goltsov, S Piraino, M P Miglietta, E I Rogaev
Turritopsis dohrnii (Cnidaria, Hydrozoa, Hydroidolina, Anthoathecata) is the only known metazoan that is capable of reversing its life cycle via morph rejuvenation from the adult medusa stage to the juvenile polyp stage. Here, we present a complete mitochondrial (mt) genome sequence of T. dohrnii, which harbors genes for 13 proteins, two transfer RNAs, and two ribosomal RNAs. The T. dohrnii mt genome is characterized by typical features of species in the Hydroidolina subclass, such as a high A+T content (71...
November 11, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27820907/box-jellyfish-alatina-alata-has-a-circumtropical-distribution
#13
Jonathan W Lawley, Cheryl Lewis Ames, Bastian Bentlage, Angel Yanagihara, Roger Goodwill, Ehsan Kayal, Kikiana Hurwitz, Allen G Collins
Species of the box jellyfish (Cubozoa) genus Alatina are notorious for their sting along the beaches of several localities of the Atlantic and Pacific. These species include Alatina alata on the Caribbean Island of Bonaire (the Netherlands), A. moseri in Hawaii, and A. mordens in Australia. Most cubozoans inhabit coastal waters, but Alatina is unusual in that specimens have also been collected in the open ocean at great depths. Alatina is notable in that populations form monthly aggregations for spermcast mating in conjunction with the lunar cycle...
October 2016: Biological Bulletin
https://www.readbyqxmd.com/read/27812408/comparative-internal-anatomy-of-staurozoa-cnidaria-with-functional-and-evolutionary-inferences
#14
Lucília S Miranda, Allen G Collins, Yayoi M Hirano, Claudia E Mills, Antonio C Marques
Comparative efforts to understand the body plan evolution of stalked jellyfishes are scarce. Most characters, and particularly internal anatomy, have neither been explored for the class Staurozoa, nor broadly applied in its taxonomy and classification. Recently, a molecular phylogenetic hypothesis was derived for Staurozoa, allowing for the first broad histological comparative study of staurozoan taxa. This study uses comparative histology to describe the body plans of nine staurozoan species, inferring functional and evolutionary aspects of internal morphology based on the current phylogeny of Staurozoa...
2016: PeerJ
https://www.readbyqxmd.com/read/27811739/the-polyps-of-oceania-armata-identified-by-dna-barcoding-cnidaria-hydrozoa
#15
Peter Schuchert
The polyps of the widely distributed medusa Oceania armata have never been found in nature and only the primary polyp is known from breeding experiments. The fully developed colony is so far unknown. This report shows that DNA sequence data of the medusa stage of O. armata permits to identify several hydroid colonies from different geographic origins as the most likely polyp stage of this medusa. These hydroids had previously been misidentified as Turritopsis species, a closely related genus which also produces medusae resembling Oceania armata...
October 18, 2016: Zootaxa
https://www.readbyqxmd.com/read/27764538/comparative-evaluation-of-chemical-profiles-of-three-representative-snow-lotus-herbs-by-uplc-dad-qtof-ms-combined-with-principal-component-and-hierarchical-cluster-analyses
#16
Qi-Lei Chen, Lin Zhu, Yi-Na Tang, Hiu-Yee Kwan, Zhong-Zhen Zhao, Hu-Biao Chen, Tao Yi
Herbal healthcare products are used worldwide as relatively safe and effective alternatives to allopathic drugs. Saussurea laniceps Hand.-Mazz.(SL), S. medusa Maxim. (SM) and S. involucrata (Kar. et Kir.) Sch.Bip. (SI) are three sources of the renowned "snow lotus" Chinese Materia Medica for treating inflammatory diseases. The three species have different therapeutic effects, among which SL has been proved to be the most potent, but they are frequently confused on the market and in the academic community. An ultra-high performance liquid chromatography-diode array detector-quadrupole time of flight-mass spectrometry (UPLC-DAD-QTOF-MS) method was developed and used to analyze 49 herbal samples for species analysis and overall quality evaluation...
October 20, 2016: Drug Testing and Analysis
https://www.readbyqxmd.com/read/27696494/muscle-and-nerve-net-organization-in-stalked-jellyfish-medusozoa-staurozoa
#17
Hannah E Westlake, Louise R Page
Staurozoan cnidarians display an unusual combination of polyp and medusa characteristics and their morphology may be informative about the evolutionary origin of medusae. We studied neuromuscular morphology of two staurozoans, Haliclystus 'sanjuanensis' and Manania handi, using whole mount immunohistochemistry with antibodies against FMRFamide and α-tubulin to label neurons and phalloidin to label muscles. All muscles appeared to lack striations. Longitudinal interradial muscles are probable homologues of stalk muscles in scyphopolyps, but in adult staurozoans they are elaborated to inwardly flex marginal lobes of the calyx during prey capture; these muscles are pennate in M...
January 2017: Journal of Morphology
https://www.readbyqxmd.com/read/27685330/associations-between-an-invasive-plant-taeniatherum-caput-medusae-medusahead-and-soil-microbial-communities
#18
Elise S Gornish, Noah Fierer, Albert Barberán
Understanding plant-microbe relationships can be important for developing management strategies for invasive plants, particularly when these relationships interact with underlying variables, such as habitat type and seedbank density, to mediate control efforts. In a field study located in California, USA, we investigated how soil microbial communities differ across the invasion front of Taeniatherum caput-medusae (medusahead), an annual grass that has rapidly invaded most of the western USA. Plots were installed in habitats where medusahead invasion is typically successful (open grassland) and typically not successful (oak woodland)...
2016: PloS One
https://www.readbyqxmd.com/read/27678847/caput-medusae
#19
W M Al Ghafri, M N Al Shukri
No abstract text is available yet for this article.
November 2015: Journal of Minimally Invasive Gynecology
https://www.readbyqxmd.com/read/27639479/phylogenetic-relationships-of-proboscoida-broch-1910-cnidaria-hydrozoa-are-traditional-morphological-diagnostic-characters-relevant-for-the-delimitation-of-lineages-at-the-species-genus-and-family-levels
#20
Amanda F Cunha, Allen G Collins, Antonio C Marques
Overlapping variation of morphological characters can lead to misinterpretation in taxonomic diagnoses and the delimitation of different lineages. This is the case for hydrozoans that have traditionally been united in the family Campanulariidae, a group known for its wide morphological variation and complicated taxonomic history. In a recently proposed phylogenetic classification of leptothecate hydrozoans, this family was restricted to a more narrow sense while a larger clade containing most species traditionally classified in Campanulariidae, along with members of Bonneviellidae, was established as the suborder Proboscoida...
September 14, 2016: Molecular Phylogenetics and Evolution
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