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https://www.readbyqxmd.com/read/28087768/the-rice-paradox-multiple-origins-but-single-domestication-in-asian-rice
#1
Jae Young Choi, Adrian E Platts, Dorian Q Fuller, Yue-Ie Hsing, Rod A Wing, Michael D Purugganan
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28086872/dapagliflozin-decreases-small-dense-low-density-lipoprotein-cholesterol-and-increases-high-density-lipoprotein-2-cholesterol-in-patients-with-type-2-diabetes-comparison-with-sitagliptin
#2
Toshiyuki Hayashi, Tomoyasu Fukui, Noriko Nakanishi, Saki Yamamoto, Masako Tomoyasu, Anna Osamura, Makoto Ohara, Takeshi Yamamoto, Yasuki Ito, Tsutomu Hirano
BACKGROUND: The sodium-glucose co-transporter-2 (SGLT-2) inhibitors have been reported to increase both low-density lipoprotein (LDL) and high-density lipoprotein (HDL)-cholesterol (C). This study aimed to determine how SGLT-2 inhibitors affect LDL and HDL-C subspecies. METHODS: This single center, open-label, randomized, prospective study included 80 patients with type 2 diabetes taking prescribed oral hypoglycemic agents. Patients were allocated to receive dapagliflozin (n = 40) or sitagliptin (n = 40) as add-on treatment...
January 13, 2017: Cardiovascular Diabetology
https://www.readbyqxmd.com/read/28086785/whole-genome-resequencing-reveals-diagnostic-markers-for-investigating-global-migration-and-hybridization-between-minke-whale-species
#3
Ketil Malde, Bjørghild B Seliussen, María Quintela, Geir Dahle, Francois Besnier, Hans J Skaug, Nils Øien, Hiroko K Solvang, Tore Haug, Rasmus Skern-Mauritzen, Naohisa Kanda, Luis A Pastene, Inge Jonassen, Kevin A Glover
BACKGROUND: In the marine environment, where there are few absolute physical barriers, contemporary contact between previously isolated species can occur across great distances, and in some cases, may be inter-oceanic. An example of this can be seen in the minke whale species complex. Antarctic minke whales are genetically and morphologically distinct from the common minke found in the north Atlantic and Pacific oceans, and the two species are estimated to have been isolated from each other for 5 million years or more...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081160/estimates-of-abundance-and-trend-of-chilean-blue-whales-off-isla-de-chilo%C3%A3-chile
#4
Barbara Galletti Vernazzani, Jennifer A Jackson, Elsa Cabrera, Carole A Carlson, Robert L Brownell
Since 1970, blue whales (Balaenoptera musculus) have been seen feeding in the waters off southern Chile during the summer and autumn (December to May). Investigation of the genetic, acoustic and morphological characteristics of these blue whales shows that they are a distinct but unnamed subspecies, called the Chilean blue whales. Photo-identification surveys have been conducted in the waters off northwestern Isla Grande de Chiloé, southern Chile from 2004-2012 and Isla Chañaral, central Chile in 2012. Over this time, 1,070 blue whales were encountered yielding, after photo-quality control, 318 and 267 unique photographs of the left and right side of the flank respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28077207/proposal-to-reclassify-roseivirga-ehrenbergii-nedashkovskaya-et-al-2008-as-roseivirga-seohaensis-comb-nov-description-of-roseivirga-seohaensis-subsp-aquiponti-subsp-nov-and-emendation-of-the-genus-roseivirga
#5
Chitra Selvaratnam, Suganthi Thevarajoo, Kian Mau Goh, Kok-Gan Chan, Chun Shiong Chong
The genus Roseivirga currently includes five species: Roseivirga ehrenbergii, R. echinicomitans, R. spongicola, R. marina and R. maritima. Marinicola seohaensis SW-152T was renamed as Roseivirgaseohaensis SW-152T and then reclassified again as a later heterotypic synonym of R. ehrenbergii KMM 6017T. In this study, based on average nucleotide identity and digital DNA-DNA hybridization values obtained from in silico methods, together with fatty acid analyses and biochemical tests, we propose to reclassify R. ehrenbergii SW-152 as Roseivirga seohaensis comb...
December 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28070308/the-seroprevalence-of-mycobacterium-avium-subspecies-paratuberculosis-in-dairy-cattle-in-xinjiang-northwest-china
#6
Xianxia Liu, Jianjun Li, Xueyun Yang, Dengfeng Wang, Jianmei Wang, Jianyong Wu
BACKGROUND: Mycobacterium avium subspecies paratuberculosis (MAP) causes chronic, wasting, and progressive enteritis in cattle, bringing significant economic losses in livestock industries. MAP has spread worldwide mainly due to movement of animals. The objective of this study was to determine the MAP seroprevalence in cattle in the Xinjiang Uygur Autonomous Region, Northwest China, and evaluate the difference between intensive farming herds (cattle number in a herd is more than 200, and the cattle cannot have access to pasture) and free-range herds (the cattle are bred by individual households, a herd is defined as the cattle are bred in a village or town in this study)...
2017: Irish Veterinary Journal
https://www.readbyqxmd.com/read/28068343/the-fleas-siphonaptera-in-iran-diversity-host-range-and-medical-importance
#7
Naseh Maleki-Ravasan, Samaneh Solhjouy-Fard, Jean-Claude Beaucournu, Anne Laudisoit, Ehsan Mostafavi
BACKGROUND: Flea-borne diseases have a wide distribution in the world. Studies on the identity, abundance, distribution and seasonality of the potential vectors of pathogenic agents (e.g. Yersinia pestis, Francisella tularensis, and Rickettsia felis) are necessary tools for controlling and preventing such diseases outbreaks. The improvements of diagnostic tools are partly responsible for an easier detection of otherwise unnoticed agents in the ectoparasitic fauna and as such a good taxonomical knowledge of the potential vectors is crucial...
January 9, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28065661/generalism-in-modern-subspecializing-medicine
#8
Marcel Levi
INTRODUCTION: Medicine is currently developing at a breath holding pace. Diseases and medical conditions for which no remedy was available only a few years ago, can now be treated or even completely cured. However, this advancement of medicine comes with increasing complexity in many situations. AIM AND METHOD: This article discusses how we have to adapt our health care organization and our work as physicians to better cope with the new challenges of the enormous advancement of medicine, with a specific focus on internal medicine...
January 5, 2017: European Journal of Internal Medicine
https://www.readbyqxmd.com/read/28065551/unsustainable-human-induced-injuries-to-the-critically-endangered-taiwanese-humpback-dolphins-sousa-chinensis-taiwanensis
#9
John Y Wang, Kimberly N Riehl, Shih Chu Yang, Claryana Araújo-Wang
The Critically Endangered Taiwanese humpback dolphin (Sousa chinensis taiwanensis) is endemic to inshore and estuarine waters of central western Taiwan. It numbers fewer than 75 individuals, is declining and faces a myriad of human threats. Data from a long-term photo-identification program on these dolphins allowed major injuries to be examined quantitatively. A large proportion (57.7%) of individuals had suffered major human-induced injuries that likely compromised their health, survivorship or reproductive potential and thus, the future of this subspecies...
January 5, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28062983/morphology-and-molecules-reveal-the-alien-posthodiplostomum-centrarchi-hoffman-1958-as-the-third-species-of-posthodiplostomum-dubois-1936-digenea-diplostomidae-in-europe
#10
Borislav Stoyanov, Simona Georgieva, Plamen Pankov, Olena Kudlai, Aneta Kostadinova, Boyko B Georgiev
Metacercariae of two species of Posthodiplostomum Dubois, 1936 (Digenea: Diplostomidae) were subjected to morphological and molecular studies: P. brevicaudatum (von Nordmann, 1832) from Gasterosteus aculeatus (L.) (Gasterosteiformes: Gasterosteidae), Bulgaria (morphology, cox1 and ITS1-5.8S-ITS2) and Perca fluviatilis L. (Perciformes: Percidae), Czech Republic (morphology, cox1, ITS1-5.8S-ITS2 and 28S); and P. centrarchi Hoffman, 1958 from Lepomis gibbosus (L.) (Perciformes: Centrarchidae), Bulgaria (morphology, cox1 and ITS1-5...
January 2017: Systematic Parasitology
https://www.readbyqxmd.com/read/28055138/aphid-specialization-on-different-summer-hosts-is-associated-with-strong-genetic-differentiation-and-unequal-symbiont-communities-despite-a-common-mating-habitat
#11
Christoph Vorburger, Jenny Herzog, Romain Rouchet
Specialization on different host plants can promote evolutionary diversification of herbivorous insects. Work on pea aphids (Acyrthosiphon pisum) has contributed significantly to the understanding of this process, demonstrating that populations associated with different host plants exhibit performance trade-offs across hosts, show adaptive host choice and genetic differentiation, and possess different communities of bacterial endosymbionts. Populations specialized on different secondary host plants during the parthenogenetic summer generations are also described for the black bean aphid (Aphis fabae complex) and are usually treated as different (morphologically cryptic) subspecies...
January 5, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28045891/susceptibility-and-antibody-response-of-the-laboratory-model-zebra-finch-taeniopygia-guttata-to-west-nile-virus
#12
Erik K Hofmeister, Melissa Lund, Valerie Shearn-Bochsler, Christopher N Balakrishnan
Since the introduction of West Nile virus (WNV) into North America in 1999 a number of passerine bird species have been found to play a role in the amplification of the virus. Arbovirus surveillance, observational studies and experimental studies have implicated passerine birds (songbirds, e.g., crows, American robins, house sparrows, and house finches) as significant reservoirs of WNV in North America, yet we lack a tractable passerine animal model for controlled studies of the virus. The zebra finch (Taeniopygia guttata) serves as a model system across a diversity of fields, and here we develop the zebra finch a songbird model for WNV...
2017: PloS One
https://www.readbyqxmd.com/read/28045086/comparative-genome-analyses-of-mycobacterium-avium-reveal-genomic-features-of-its-subspecies-and-strains-that-cause-progression-of-pulmonary-disease
#13
Kei-Ichi Uchiya, Shuta Tomida, Taku Nakagawa, Shoki Asahi, Toshiaki Nikai, Kenji Ogawa
Pulmonary disease caused by nontuberculous mycobacteria (NTM) is increasing worldwide. Mycobacterium avium is the most clinically significant NTM species in humans and animals, and comprises four subspecies: M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS), M. avium subsp. paratuberculosis (MAP), and M. avium subsp. hominissuis (MAH). To improve our understanding of the genetic landscape and diversity of M. avium and its role in disease, we performed a comparative genome analysis of 79 M. avium strains...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043575/rapid-identification-of-mycobacterium-avium-ssp-paratuberculosis-laboratory-strains-by-is900-nested-polymerase-chain-reaction
#14
Mohammad Mohammad Taheri, Nader Mosavari, Mohammad Mehdi Feizabadi, Keyvan Tadayon, Rouholah Keshavarz, Reza Aref Pajoohi, Kioomars Soleimani, Shojaat Dashti Pour
INTRODUTION: Mycobacterium avium ssp paratuberculosis (MAP) causes paratuberculosis (Johne's disease) in ruminants. As a species, M. avium comprises M. avium subsp. hominissuis and a number of clones that are known to have evolved from this subspecies, namely M. avium subsp. avium (MAA), M. avium subsp. silvaticum, and MAP. Despite the very high genomic similarity of MAP and MAA, the insertion sequence IS900, which is 1,451-bp long, is now understood to be exclusively present in 10-20 copies in the genome of MAP...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28043571/genotyping-analysis-of-bovine-ovine-and-caprine-paratuberculosis-in-iran-an-is900-rflp-study
#15
Lida Abdolmohammadi Khiav, Masoud Haghkhah, Keyvan Tadayon, Nader Mosavari
OBJECTIVE/BACKGROUND: Mycobacterium avium subspecies paratuberculosis (MAP) has been reported in Iranian cattle since 1965. Little is known on the population genetics of MAP in this Middle-Eastern State. A principle scope of this study was therefore genetic characterization of MAP isolates collected from farm animals in Iran. METHODS: Sixteen field isolates of MAP collected from bovine (n=8), ovine (n=3), and caprine (n=2) hosts in Alborz, Fars, Isfahan, Qazvin, Tehran, and Zanjan provinces were subcultured on mycobactin J-supplemented Herrold's egg slopes in order to provide the required genomic material...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28043561/identification-of-different-subtypes-of-rapid-growing-atypical-mycobacterium-from-water-and-soil-sources-using-pcr-rflp-using-hsp65-and-rrna-16s-23s-genes
#16
Mohammad Varahram, Parissa Farnia, Shima Saif, Mehran Marashian, Poopak Farnia, Jaladein Ghanavi, Ali Akbar Velayati
OBJECTIVE/BACKGROUND: Nontuberculosis mycobacteria (NTM) are a diverse group of microorganisms that cause a variety of diseases in humans including skin, respiratory, and gastrointestinal tract infection. Generally, NTM are classified into two categories: rapid (<7days) and slow growing (>7days). In this study, we aimed to investigate NTM frequency and prevalence in environmental samples. Additionally, we tried to identify various subtypes of isolated rapid growing mycobacteria (RGM)...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28039891/atmospheric-deposition-exposes-qinling-pandas-to-toxic-pollutants
#17
Yi-Ping Chen, Ying-Juan Zheng, Qiang Liu, Yi Song, Zhi-Sheng An, Qing-Yi Ma, Aaron M Ellison
The giant panda (Ailuropoda melanoleuca) is one of the most endangered animals in the world, and it is recognized worldwide as a symbol for conservation. A previous study showed that wild and captive pandas, especially those of the Qinling subspecies, were exposed to toxicants in their diet of bamboo; the ultimate origin of these toxicants is unknown. Here we show that atmospheric deposition is the most likely origin of heavy metals and persistent organic pollutants (POPs) in the diets of captive and wild Qinling pandas...
December 31, 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28038939/skin-fragility-in-the-wild-derived-inbred-mouse-strain-mus-pahari-eij
#18
C Herbert Pratt, Christopher S Potter, Thomas J Sproule, Raoul V Kuiper, Son Yong Karst, Soheil S Dadras, Derry C Roopenian, John P Sundberg
Mus pahari is a wild-derived, inbred mouse strain. M. pahari colony managers observed fragility of this strain's skin resulting in separation of tail skin from the mouse if handled incorrectly. Tail skin tension testing of M. pahari resulted in significantly lowered force threshold for caudal skin rupture and loss in comparison to closely related inbred mouse species and subspecies and even more than a model for junctional epidermolysis bullosa. Histologically, the tail skin separated at the subdermal level with the dermis firmly attached to the epidermis, excluding the epidermolysis bullosa complex of diseases...
December 27, 2016: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28036146/behavioral-response-to-song-and-genetic-divergence-in-two-subspecies-of-white-crowned-sparrows-zonotrichia-leucophrys
#19
Sara E Lipshutz, Isaac A Overcast, Michael J Hickerson, Robb T Brumfield, Elizabeth P Derryberry
Divergence in sexual signals may drive reproductive isolation between lineages, but behavioral barriers can weaken in contact zones. Here, we investigate the role of song as a behavioral and genetic barrier in a contact zone between two subspecies of white-crowned sparrows (Zonotrichia leucophrys). We employed a reduced genomic dataset to assess population structure and infer the history underlying divergence, gene flow and hybridization. We also measured divergence in song and tested behavioral responses to song using playback experiments within and outside the contact zone...
December 30, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28033346/improving-phylogeny-reconstruction-at-the-strain-level-using-peptidome-datasets
#20
Aitor Blanco-Míguez, Jan P Meier-Kolthoff, Alberto Gutiérrez-Jácome, Markus Göker, Florentino Fdez-Riverola, Borja Sánchez, Anália Lourenço
Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution...
December 2016: PLoS Computational Biology
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