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https://www.readbyqxmd.com/read/29215911/weird-animals-sex-and-genome-evolution
#1
Jennifer A Marshall Graves
Making my career in Australia exposed me to the tyranny of distance, but it gave me opportunities to study our unique native fauna. Distantly related animal species present genetic variation that we can use to explore the most fundamental biological structures and processes. I have compared chromosomes and genomes of kangaroos and platypus, tiger snakes and emus, devils (Tasmanian) and dragons (lizards). I particularly love the challenges posed by sex chromosomes, which, apart from determining sex, provide stunning examples of epigenetic control and break all the evolutionary rules that we currently understand...
December 7, 2017: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/29180746/numts-colonization-in-mammalian-genomes
#2
F M Calabrese, D L Balacco, R Preste, M A Diroma, R Forino, M Ventura, M Attimonelli
The colonization of the nuclear genome by mitochondrial DNA is an ongoing process in eukaryotes and plays an important role in genomic variability. Notwithstanding the DNA sequence availability of about 100 complete eukaryotic genomes, up to now NumtS distribution has been fully reported for a small number of sequenced eukaryotic species. With the aim to clarify the time and way of NumtS evolution, we explored the genomic distribution of NumtS in 23 eukaryotic species using an intra/interspecies in silico approach based on a cross-species similarity search and deeply investigate the evolution of NumtS in mammals...
November 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29161408/landscape-of-dna-methylation-on-the-marsupial-x
#3
Shafagh A Waters, Alexandra M Livernois, Hardip Patel, Denis O'Meally, Jeff M Craig, Jennifer A Marshall Graves, Catherine M Suter, Paul D Waters
DNA methylation plays a key role in maintaining transcriptional silence on the inactive X chromosome of eutherian mammals. Beyond eutherians, there are limited genome wide data on DNA methylation from other vertebrates. Previous studies of X borne genes in various marsupial models revealed no differential DNA methylation of promoters between the sexes, leading to the conclusion that CpG methylation plays no role in marsupial X-inactivation. Using reduced representation bisulfite sequencing, we generated male and female CpG methylation profiles in four representative vertebrates (mouse, gray short-tailed opossum, platypus and chicken)...
November 17, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29032097/comparative-assessment-of-the-adverse-outcome-of-wastewater-effluents-by-integrating-oxidative-stress-and-histopathological-alterations-in-endemic-fish
#4
Palas Samanta, Hyungjoon Im, Jisu Yoo, Hwanggoo Lee, Nan-Young Kim, Wonky Kim, Soon-Jin Hwang, Woo-Keun Kim, Jinho Jung
This study evaluated the adverse effect of wastewater effluents on three fish species, Carassius auratus, Zacco platypus, and Zacco koreanus, collected in the Eungcheon, Mihocheon, and Busocheon streams, respectively. Fish gills, liver, and kidneys from the mixing zone (MZ) and sites upstream (US) and downstream (DS) of the MZ were analyzed for oxidative stress responses and histology. Catalase and glutathione S-transferase activity was significantly higher at MZ and DS than from US (p<0.05), indicating induction of antioxidant defense mechanisms...
October 8, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/29026079/a-long-range-cis-regulatory-element-for-class-i-odorant-receptor-genes
#5
Tetsuo Iwata, Yoshihito Niimura, Chizuru Kobayashi, Daichi Shirakawa, Hikoyu Suzuki, Takayuki Enomoto, Kazushige Touhara, Yoshihiro Yoshihara, Junji Hirota
Individual olfactory sensory neurons express a single odorant receptor gene from either class I genes residing in a single cluster on a single chromosome or class II genes spread over multiple clusters on multiple chromosomes. Here, we identify an enhancer element for mouse class I genes, the J element, that is conserved through mammalian species from the platypus to humans. The J element regulates most class I genes expression by exerting an effect over ~ 3 megabases within the whole cluster. Deletion of the trans J element increases the expression frequencies of class I genes from the intact J allele, indicating that the allelic exclusion of class I genes depends on the activity of the J element...
October 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28949902/marsupial-and-monotreme-cathelicidins-display-antimicrobial-activity-including-against-methicillin-resistant-staphylococcus-aureus
#6
Emma Peel, Yuanyuan Cheng, Julianne T Djordjevic, Michael Kuhn, Tania Sorrell, Katherine Belov
With the growing demand for new antibiotics to combat increasing multi-drug resistance, a family of antimicrobial peptides known as cathelicidins has emerged as potential candidates. Expansions in cathelicidin-encoding genes in marsupials and monotremes are of specific interest as the peptides they encode have evolved to protect immunologically naive young in the harsh conditions of the pouch and burrow. Our previous work demonstrated that some marsupial and monotreme cathelicidins have broad-spectrum antibacterial activity and kill resistant bacteria, but the activity of many cathelicidins is unknown...
September 27, 2017: Microbiology
https://www.readbyqxmd.com/read/28922870/male-mutation-bias-is-the-main-force-shaping-chromosomal-substitution-rates-in-monotreme-mammals
#7
Vivian Link, Diana Aguilar-Gómez, Ciro Ramírez-Suástegui, Laurence D Hurst, Diego Cortez
In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Male mutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28919547/deep-sequencing-to-resolve-complex-diversity-of-apicomplexan-parasites-in-platypuses-and-echidnas-proof-of-principle-for-wildlife-disease-investigation
#8
Jan Šlapeta, Stefan Saverimuttu, Larry Vogelnest, Cheryl Sangster, Frances Hulst, Karrie Rose, Paul Thompson, Richard Whittington
The short-beaked echidna (Tachyglossus aculeatus) and the platypus (Ornithorhynchus anatinus) are iconic egg-laying monotremes (Mammalia: Monotremata) from Australasia. The aim of this study was to demonstrate the utility of diversity profiles in disease investigations of monotremes. Using small subunit (18S) rDNA amplicon deep-sequencing we demonstrated the presence of apicomplexan parasites and confirmed by direct and cloned amplicon gene sequencing Theileria ornithorhynchi, Theileria tachyglossi, Eimeria echidnae and Cryptosporidium fayeri...
September 13, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28854623/extreme-mitogenomic-variation-in-natural-populations-of-chaetognaths
#9
Ferdinand Marlétaz, Yannick Le Parco, Shenglin Liu, Katja T C A Peijnenburg
The extent of within-species genetic variation across the diversity of animal life is an underexplored problem in ecology and evolution. Although neutral genetic variation should scale positively with population size, mitochondrial diversity levels are believed to show little variation across animal species. Here, we report an unprecedented case of extreme mitochondrial diversity within natural populations of two morphospecies of chaetognaths (arrow worms). We determine that this diversity is composed of deep sympatric mitochondrial lineages, which are in some cases as divergent as human and platypus...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28839019/draft-genome-sequence-of-the-fungus-associated-with-oak-wilt-mortality-in-south-korea-raffaelea-quercus-mongolicae-kacc44405
#10
Jongbum Jeon, Ki-Tae Kim, Hyeunjeong Song, Gir-Won Lee, Kyeongchae Cheong, Hyunbin Kim, Gobong Choi, Yong-Hwan Lee, Jane E Stewart, Ned B Klopfenstein, Mee-Sook Kim
The fungus Raffaelea quercus-mongolicae is the causal agent of Korean oak wilt, a disease associated with mass mortality of oak trees (e.g., Quercus spp.). The fungus is vectored and dispersed by the ambrosia beetle, Platypus koryoensis Here, we present the 27.0-Mb draft genome sequence of R. quercus-mongolicae strain KACC44405.
August 24, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28683451/sleep-related-electrophysiology-and-behavior-of-tinamous-eudromia-elegans-tinamous-do-not-sleep-like-ostriches
#11
Ryan K Tisdale, Alexei L Vyssotski, John A Lesku, Niels C Rattenborg
The functions of slow wave sleep (SWS) and rapid eye movement (REM) sleep, distinct sleep substates present in both mammals and birds, remain unresolved. One approach to gaining insight into their function is to trace the evolution of these states through examining sleep in as many taxonomic groups as possible. The mammalian and avian clades are each composed of two extant groups, i.e., the monotremes (echidna and platypus) and therian (marsupial and eutherian [or placental]) mammals, and Palaeognaths (cassowaries, emus, kiwi, ostriches, rheas, and tinamous) and Neognaths (all other birds) among birds...
2017: Brain, Behavior and Evolution
https://www.readbyqxmd.com/read/28683132/evolutionary-analysis-of-fam83h-in-vertebrates
#12
Wushuang Huang, Mei Yang, Changning Wang, Yaling Song
Amelogenesis imperfecta is a group of disorders causing abnormalities in enamel formation in various phenotypes. Many mutations in the FAM83H gene have been identified to result in autosomal dominant hypocalcified amelogenesis imperfecta in different populations. However, the structure and function of FAM83H and its pathological mechanism have yet to be further explored. Evolutionary analysis is an alternative for revealing residues or motifs that are important for protein function. In the present study, we chose 50 vertebrate species in public databases representative of approximately 230 million years of evolution, including 1 amphibian, 2 fishes, 7 sauropsidas and 40 mammals, and we performed evolutionary analysis on the FAM83H protein...
2017: PloS One
https://www.readbyqxmd.com/read/28652620/differential-cohesin-loading-marks-paired-and-unpaired-regions-of-platypus-sex-chromosomes-at-prophase-i
#13
Aaron E Casey, Tasman J Daish, Jose Luis Barbero, Frank Grützner
Cohesins are vital for chromosome organisation during meiosis and mitosis. In addition to the important function in sister chromatid cohesion, these complexes play key roles in meiotic recombination, DSB repair, homologous chromosome pairing and segregation. Egg-laying mammals (monotremes) feature an unusually complex sex chromosome system, which raises fundamental questions about organisation and segregation during meiosis. We discovered a dynamic and differential accumulation of cohesins on sex chromosomes during platypus prophase I and specific reorganisation of the sex chromosome complex around a large nucleolar body...
June 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28484364/energy-homeostasis-in-monotremes
#14
REVIEW
Stewart C Nicol
In 1803, the French anatomist Étienne Geoffroy Saint-Hilaire decided that the newly described echidna and platypus should be placed in a separate order, the monotremes, intermediate between reptiles and mammals. The first physiological observations showed monotremes had low body temperatures and metabolic rates, and the consensus was that they were at a stage of physiological development intermediate between "higher mammals" and "lower vertebrates." Subsequent studies demonstrated that platypuses and echidnas are capable of close thermoregulation in the cold although less so under hot conditions...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28474185/occurrence-and-distribution-of-yellow-grub-trematodes-clinostomum-complanatum-infection-in-taiwan
#15
Mao-Lin Wang, Hui-Yu Chen, Hsiu-Hui Shih
Digenetic trematodes of the genus Clinostomum are widely distributed in many species of freshwater fish and are known to cause the zoonotic disease Halzoun. Humans may become accidental hosts if they ingest raw freshwater fish containing metacercaria of Clinostomum complanatum, which causes pharyngitis or laryngitis. The yellow grub parasitizing cultivated ayu (Plecoglossus altivelis) and loach (Misgurnus anguillicaudatus) was one of the most serious problems in fish farms from 1977 to 1979 in Taiwan. The present study revealed, for the first time, frequent occurrence of C...
June 2017: Parasitology Research
https://www.readbyqxmd.com/read/28464621/infants-adapt-to-speaking-rate-differences-in-word-segmentation
#16
Yuanyuan Wang, Fernando Llanos, Amanda Seidl
Throughout their development, infants are exposed to varying speaking rates. Thus, it is important to determine whether they are able to adapt to speech at varying rates and recognize target words from continuous speech despite speaking rate differences. To address this question, a series of four experiments were conducted to test whether infants can recognize words in continuous speech when rate is variable. In addition, the underlying mechanisms that infants may use to cope with variations induced by different speaking rates were also examined...
April 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28299878/igy-a-key-isotype-in-antibody-evolution
#17
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
#18
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
#19
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 Research
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
#20
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...
May 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
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