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https://www.readbyqxmd.com/read/28299878/igy-a-key-isotype-in-antibody-evolution
#1
Xiaoying Zhang, Rosaleen A Calvert, Brian J Sutton, Katy A Doré
Immunoglobulin Y (IgY) is central to our understanding of immunoglobulin evolution. It has links to antibodies from the ancestral IgM to the mucosal IgX and IgA, as well as to mammalian serum IgG and IgE. IgY is found in amphibians, birds and reptiles, and as their most abundant serum antibody, is orthologous to mammalian IgG. However, IgY has the same domain architecture as IgM and IgE, lacking a hinge region and comprising four heavy-chain constant domains. The relationship between IgY and the mucosal antibodies IgX and IgA is discussed herein, in particular the question of how IgA could have contributed to the emergence of IgY...
March 16, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28283047/pluto-and-the-platypus-an-odd-ball-and-an-odd-duck-on-classificatory-norms
#2
Matthew H Slater
Many astronomers seem to believe that we have discovered that Pluto is not a planet. I contest this assessment. Recent discoveries of trans-Neptunian Pluto-sized objects do not militate for Pluto's expulsion from the planets unless we have prior reason for not simply counting these newly-discovered objects among the planets. I argue that this classificatory controversy - which I compare to the controversy about the classification of the platypus - illustrates how our classificatory practices are laden with normative commitments of a distinctive kind...
February 2017: Studies in History and Philosophy of Science
https://www.readbyqxmd.com/read/28239666/making-the-most-of-rna-seq-pre-processing-sequencing-data-with-opossum-for-reliable-snp-variant-detection
#3
Laura Oikkonen, Stefano Lise
Identifying variants from RNA-seq (transcriptome sequencing) data is a cost-effective and versatile alternative to whole-genome sequencing. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller...
January 17, 2017: Wellcome Open Res
https://www.readbyqxmd.com/read/28191733/a-novel-dynamic-expression-of-vasa-in-male-germ-cells-during-spermatogenesis-in-the-chinese-soft-shell-turtle-pelidiscus-sinensis
#4
Wei Li, Piaoyi Zhang, Xuling Wu, Xinping Zhu, Hongyan Xu
vasa gene encodes a highly conserved DEAD-box RNA helicase, required for germ cell development across animal kingdom. Vasa mutations cause male infertility in mammals. It has been widely used as a biomarker for studying animal fertility or manipulating germ cells in organisms. However, in reptilians, the functions of vasa gene involved in germ cell differentiation are largely unclear; this hampers the development of biological techniques and the improvement of the productivity in these species. Here a vasa cDNA was isolated in Chinese soft-shell turtle and it predicts a protein of 691 amino acid residues, which is 72%, 69%, 58%, 59%, and 54-56% identical to its homolog from mouse, platypus, frog, chicken, and fish, respectively, and named as PsVasa...
February 13, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28139954/a-need-for-dynamic-hematology-and-serum-biochemistry-reference-tools-novel-use-of-sine-wave-functions-to-produce-seasonally-varying-reference-curves-in-platypuses-ornithorhynchus-anatinus
#5
James W Macgregor, Carly S Holyoake, Joanne H Connolly, Ian D Robertson, Patricia A Fleming, Kristin S Warren
Seasonal changes in hematology and serum biochemistry results, described by separate reference intervals for different seasons, have been reported in many animals. We developed a novel method to investigate seasonal variation in values and a reference tool (the reference curve) based on sine wave functions that, for suitable variables, represents data more appropriately than a fixed reference interval. We applied these techniques to values observed in blood samples from 126 adult wild platypuses ( Ornithorhynchus anatinus ) (58 females and 68 males)...
January 31, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28118556/investigation-into-individual-health-and-exposure-to-infectious-agents-of-platypuses-ornithorhynchus-anatinus-in-two-river-catchments-in-northwest-tasmania
#6
James W Macgregor, Carly S Holyoake, Sarah A Munks, Joanne H Connolly, Ian D Robertson, Patricia A Fleming, Kristin S Warren
Changes in the health of individuals within wildlife populations can be a cause or effect of population declines in wildlife species. Aspects of individual platypus ( Ornithorhynchus anatinus ) health have been reported. However, holistic studies investigating potential synergistic effects of both pathogens and environmental factors are needed to expand understanding of platypus individual health. We collected baseline data on the health of platypuses in two Tasmanian river catchments (including evidence of the potentially fatal fungal disease mucormycosis) and on individual, demographic, geographic, and temporal patterns associated with health data results...
January 24, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28105919/snoreport-2-0-new-features-and-a-refined-support-vector-machine-to-improve-snorna-identification
#7
João Victor de Araujo Oliveira, Fabrizio Costa, Rolf Backofen, Peter Florian Stadler, Maria Emília Machado Telles Walter, Jana Hertel
BACKGROUND: snoReport uses RNA secondary structure prediction combined with machine learning as the basis to identify the two main classes of small nucleolar RNAs, the box H/ACA snoRNAs and the box C/D snoRNAs. Here, we present snoReport 2.0, which substantially improves and extends in the original method by: extracting new features for both box C/D and H/ACA box snoRNAs; developing a more sophisticated technique in the SVM training phase with recent data from vertebrate organisms and a careful choice of the SVM parameters C and γ; and using updated versions of tools and databases used for the construction of the original version of snoReport...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103801/parasite-infection-of-public-databases-a-data-mining-approach-to-identify-apicomplexan-contaminations-in-animal-genome-and-transcriptome-assemblies
#8
Janus Borner, Thorsten Burmester
BACKGROUND: Contaminations from various exogenous sources are a common problem in next-generation sequencing. Another possible source of contaminating DNA are endogenous parasites. On the one hand, undiscovered contaminations of animal sequence assemblies may lead to erroneous interpretation of data; on the other hand, when identified, parasite-derived sequences may provide a valuable source of information. RESULTS: Here we show that sequences deriving from apicomplexan parasites can be found in many animal genome and transcriptome projects, which in most cases derived from an infection of the sequenced host specimen...
January 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28074367/assessment-of-metal-contamination-in-the-hun-river-china-and-evaluation-of-the-fish-zacco-platypus-and-the-snail-radix-swinhoei-as-potential-biomonitors
#9
Xing Wu, Shaofeng Wang, Hongxing Chen, Zhiqiang Jiang, Hongwei Chen, Mi Gao, Ran Bi, Paul L Klerks, He Wang, Yongju Luo, Lingtian Xie
The Hun River is a major tributary of the Liao River in the northeast area of China and provides drinking water for 23 million local residents. This study was designed to assess the severity of metal contamination in the Hun River and the potential use of indigenous organisms (the fish Zacco platypus and the snail Radix swinhoei) as biomonitors of metal contamination. Water, sediment, and the native fish and snails were collected at four sampling sites that differed in their physicochemical characteristics and their contamination levels...
January 10, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28062306/platypus-and-opossum-calcitonins-exhibit-strong-activities-even-though-they-belong-to-mammals
#10
Teruhito Yamashita, Nobuyuki Udagawa, Gnanasagar Janardhanan Thirukonda, Shunsuke Uehara, Hirose Yamauchi, Nobuo Suzuki, Feng Li, Yasuhiro Kobayashi, Naoyuki Takahashi
In mammalian assay systems, calcitonin peptides of non-mammalian species exhibit stronger activity than those of mammals. Recently, comparative analyses of a wide-range of species revealed that platypus and opossum, which diverged early from other mammals, possess calcitonins that are more similar in amino acid sequence to those of non-mammals than mammals. We herein determined whether platypus and opossum calcitonins exhibit similar biological activities to those of non-mammalian calcitonins using an assay of actin ring formation in mouse osteoclasts...
January 3, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28053161/getprime-2-0-gene-and-transcript-specific-qpcr-primers-for-13-species-including-polymorphisms
#11
Fabrice P A David, Jacques Rougemont, Bart Deplancke
GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing gene- and transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification of one or several splice variants of most known genes. To ease selection, primers have also been ranked according to defined criteria such as genome-wide specificity (with BLAST), amplicon size, and isoform coverage. Here, we report a major upgrade (2.0) of the database: eight new species (yeast, chicken, macaque, chimpanzee, rat, platypus, pufferfish, and Anolis carolinensis) now complement the five already included in the previous version (human, mouse, zebrafish, fly, and worm)...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898108/monotreme-glucagon-like-peptide-1-in-venom-and-gut-one-gene-two-very-different-functions
#12
Enkhjargal Tsend-Ayush, Chuan He, Mark A Myers, Sof Andrikopoulos, Nicole Wong, Patrick M Sexton, Denise Wootten, Briony E Forbes, Frank Grutzner
The importance of Glucagon like peptide 1 (GLP-1) for metabolic control and insulin release sparked the evolution of genes mimicking GLP-1 action in venomous species (e.g. Exendin-4 in Heloderma suspectum (gila monster)). We discovered that platypus and echidna express a single GLP-1 peptide in both intestine and venom. Specific changes in GLP-1 of monotreme mammals result in resistance to DPP-4 cleavage which is also observed in the GLP-1 like Exendin-4 expressed in Heloderma venom. Remarkably we discovered that monotremes evolved an alternative mechanism to degrade GLP-1...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27832215/avoiding-pandemic-fears-in-the-subway-and-conquering-the-platypus
#13
COMMENT
A Gonzalez, Y Vázquez-Baeza, J B Pettengill, A Ottesen, D McDonald, R Knight
Metagenomics is increasingly used not just to show patterns of microbial diversity but also as a culture-independent method to detect individual organisms of intense clinical, epidemiological, conservation, forensic, or regulatory interest. A widely reported metagenomic study of the New York subway suggested that the pathogens Yersinia pestis and Bacillus anthracis were part of the "normal subway microbiome." In their article in mSystems, Hsu and collaborators (mSystems 1(3):e00018-16, 2016, http://dx.doi.org/10...
May 2016: MSystems
https://www.readbyqxmd.com/read/27769777/improvised-cricothyrotomy-on-a-mountain-using-hiking-gear
#14
Clare A Johnson, Diana S Goodwine, Ingrid Passier
We present a case of a 57-year-old man who fell while climbing a mountain in California and sustained severe facial trauma. Three firefighters and 2 emergency physicians witnessed the fall and resuscitated the patient. The patient ultimately required a surgical cricothyrotomy performed with a pocket knife and Platypus hydration pack. The physicians made a makeshift positive pressure airway device using the Platypus hydration pack. We believe this is the first case report describing an improvised cricothyrotomy performed in the wilderness using only hiking gear...
December 2016: Wilderness & Environmental Medicine
https://www.readbyqxmd.com/read/27757425/comparative-cranial-morphology-in-living-and-extinct-platypuses-feeding-behavior-electroreception-and-loss-of-teeth
#15
Masakazu Asahara, Masahiro Koizumi, Thomas E Macrini, Suzanne J Hand, Michael Archer
The modern platypus, Ornithorhynchus anatinus, has an eye structure similar to aquatic mammals; however, platypuses also have a "sixth sense" associated with the bill electro- and mechanoreception that they use without opening their eyes underwater. We hypothesize that Ornithorhynchus and the Miocene taxon Obdurodon have different sensory capacities, which may have resulted from differences in foraging behavior. To estimate differences in foraging, sensory systems, and anatomical divergence between these monotremes, we compared their skull morphologies...
October 2016: Science Advances
https://www.readbyqxmd.com/read/27671001/the-platypus-in-edinburgh-robert-jameson-robert-knox-and-the-place-of-the-ornithorhynchus-in-nature-1821-24
#16
Bill Jenkins
The duck-billed platypus, or Ornithorhynchus, was the subject of an intense debate among natural historians in the late eighteenth and early nineteenth centuries. Its paradoxical mixture of mammalian, avian and reptilian characteristics made it something of a taxonomic conundrum. In the early 1820s Robert Jameson (1774-1854), the professor of natural history at the University of Edinburgh and the curator of the University's natural history museum, was able to acquire three valuable specimens of this species...
October 2016: Annals of Science
https://www.readbyqxmd.com/read/27590916/an-analytical-workflow-for-accurate-variant-discovery-in-highly-divergent-regions
#17
Shulan Tian, Huihuang Yan, Claudia Neuhauser, Susan L Slager
BACKGROUND: Current variant discovery methods often start with the mapping of short reads to a reference genome; yet, their performance deteriorates in genomic regions where the reads are highly divergent from the reference sequence. This is particularly problematic for the human leukocyte antigen (HLA) region on chromosome 6p21.3. This region is associated with over 100 diseases, but variant calling is hindered by the extreme divergence across different haplotypes. RESULTS: We simulated reads from chromosome 6 exonic regions over a wide range of sequence divergence and coverage depth...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27557648/formation-and-dissociation-of-sperm-bundles-in-monotremes
#18
Brett Nixon, Heath Ecroyd, Jean-Louis Dacheux, Francoise Dacheux, Valerie Labas, Steve D Johnston, Russell C Jones
As monotremes are the earliest offshoot of the mammalian lineage, the platypus and short-beaked echidna were studied as model animals to assess the origin and biological significance of adaptations considered unique to therian mammals: epididymal maturation and subsequent capacitation. We show that spermatozoa from both species assemble into bundles of approximately 100 cells during passage through the epididymis and that an epididymal protein, secreted protein, acidic, cysteine-rich (osteonectin) (SPARC), is involved in bundle formation...
August 24, 2016: Biology of Reproduction
https://www.readbyqxmd.com/read/27505040/dermatophilus-congolensis-infection-in-platypus-ornithorhynchus-anatinus-tasmania-australia-2015
#19
Tamika Lunn, James Macgregor, Sarah Munks, Scott Carver
We report disease due to Dermatophilus congolensis infection in three of 13 (23%) platypuses ( Ornithorhynchus anatinus ) from a catchment in Tasmania, Australia. This pathogen has not previously been reported in platypuses. Two of the three infected platypuses had extensive scab formations, but no substantial hair loss was apparent.
October 2016: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/27469944/draft-genome-sequence-of-raffaelea-quercivora-jcm-11526-a-japanese-oak-wilt-pathogen-associated-with-the-platypodid-beetle-platypus-quercivorus
#20
Hayato Masuya, Ri-Ichiroh Manabe, Moriya Ohkuma, Rikiya Endoh
The Japanese oak wilt pathogen Raffaelea quercivora and the platypodid beetle, Platypus quercivorus, cause serious mass mortality of Quercus spp. in Japan. Here, we present the first draft genome sequence of R. quercivora JCM 11526 to increase our understanding of the mechanism of pathogenicity and symbiosis with the ambrosia beetle.
2016: Genome Announcements
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