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Sample records for closely related paramyxoviruses

  1. Paramyxoviruses of fish: Chapter 17

    Science.gov (United States)

    Meyers, Theodore R; Batts, William N.; Kibenge, Frederick S. B.; Godoy, Marcos

    2016-01-01

    The first fish paramyxovirus was isolated from normal adult Chinook salmon returning to a coastal hatchery in Oregon in the fall of 1982. Subsequently, the virus was isolated from other stocks of adult Chinook salmon and one stock of adult coho salmon in California, Oregon, Washington and Alaska, leading to its designation as the Pacific salmon paramyxovirus (PSPV). The slow-growing virus can be isolated from tissues and ovarian fluids of healthy adult fish returning to spawn and apparently causes no clinical signs of disease or mortality. In 1995, a different and widely disseminated paramyxovirus was isolated from farmed Atlantic salmon in Norway and was designated as Atlantic salmon paramyxovirus (ASPV). Although this virus caused no disease or mortality when injected into juvenile Atlantic salmon, ASPV has been associated with proliferative gill inflammation in sea-reared yearling fish; however, additional infectious agents may be involved in the etiology of the condition. Sequence analysis of PSPV and ASPV isolates using the polymerase gene established their placement in the family Paramyxoviridaeand has shown the two viruses to be closely related but sufficiently different from each other and from other known paramyxoviruses to possibly represent new genera within the family. The viruses can be diagnosed by isolation in cell culture with final confirmation by molecular methods. Other paramyxovirus-like agents have been observed or isolated from rainbow trout in Germany, from seabream in Japan associated with epithelial necrosis, from turbot in Spain associated with erythrocytic inclusion bodies and buccal/opercular hemorrhaging and from koi and common carp associated with gill necrosis in the European Union.

  2. Novel paramyxoviruses in free-ranging European bats.

    Directory of Open Access Journals (Sweden)

    Andreas Kurth

    Full Text Available The zoonotic potential of paramyxoviruses is particularly demonstrated by their broad host range like the highly pathogenic Hendra and Nipah viruses originating from bats. But while so far all bat-borne paramyxoviruses have been identified in fruit bats across Africa, Australia, South America, and Asia, we describe the detection and characterization of the first paramyxoviruses in free-ranging European bats. Moreover, we examined the possible impact of paramyxovirus infection on individual animals by comparing histo-pathological findings and virological results. Organs from deceased insectivorous bats of various species were sampled in Germany and tested for paramyxovirus RNA in parallel to a histo-pathological examination. Nucleic acids of three novel paramyxoviruses were detected, two viruses in phylogenetic relationship to the recently proposed genus Jeilongvirus and one closely related to the genus Rubulavirus. Two infected animals revealed subclinical pathological changes within their kidneys, suggestive of a similar pathogenesis as the one described in fruit bats experimentally infected with Hendra virus.Our findings indicate the presence of bat-born paramyxoviruses in geographic areas free of fruit bat species and therefore emphasize a possible virus-host co-evolution in European bats. Since these novel viruses are related to the very distinct genera Rubulavirus and Jeilongvirus, a similarly broad genetic diversity among paramyxoviruses in other Microchiroptera compared to Megachiroptera can be assumed. Given that the infected bats were either found in close proximity to heavily populated human habitation or areas of intensive agricultural use, a potential risk of the emergence of zoonotic paramyxoviruses in Europe needs to be considered.

  3. Molecular epidemiology of paramyxoviruses in frugivorous Eidolon helvum bats in Zambia.

    Science.gov (United States)

    Muleya, Walter; Sasaki, Michihito; Orba, Yasuko; Ishii, Akihiro; Thomas, Yuka; Nakagawa, Emiko; Ogawa, Hirohito; Hang'ombe, Bernard; Namangala, Boniface; Mweene, Aaron; Takada, Ayato; Kimura, Takashi; Sawa, Hirofumi

    2014-04-01

    In this study, we describe the detection of novel paramyxoviruses from the Eidolon helvum species of fruit bats. We extracted RNA from 312 spleen samples from bats captured in Zambia over a period of 4 years (2008-2011). Semi-nested RT-PCR detected a total of 25 (8%) positive samples for paramyxoviruses which were then directly sequenced and analyzed using phylogenetic analysis. Among the positive samples, seven novel paramyxoviruses were detected. Five viruses were closely related to the genus Henipavirus, while two viruses were related to the unclassified Bat paramyxoviruses from Ghana and Congo Brazzaville. Our study identified novel Henipavirus-related and unrelated viruses using RT-PCR in fruit bats from Kansaka National Park and indicated the presence of similar Bat paramyxoviruses originating from wide geographic areas, suggesting the ability of bats to harbor and transmit viruses. The presence of these viruses in fruit bats might pose a public health risk.

  4. Molecular epidemiology of paramyxoviruses in Zambian wild rodents and shrews.

    Science.gov (United States)

    Sasaki, Michihito; Muleya, Walter; Ishii, Akihiro; Orba, Yasuko; Hang'ombe, Bernard M; Mweene, Aaron S; Moonga, Ladslav; Thomas, Yuka; Kimura, Takashi; Sawa, Hirofumi

    2014-02-01

    Rodents and shrews are known to harbour various viruses. Paramyxoviruses have been isolated from Asian and Australian rodents, but little is known about them in African rodents. Recently, previously unknown paramyxovirus sequences were found in South African rodents. To date, there have been no reports related to the presence and prevalence of paramyxoviruses in shrews. We found a high prevalence of paramyxoviruses in wild rodents and shrews from Zambia. Semi-nested reverse transcription-PCR assays were used to detect paramyxovirus RNA in 21 % (96/462) of specimens analysed. Phylogenetic analysis revealed that these viruses were novel paramyxoviruses and could be classified as morbillivirus- and henipavirus-related viruses, and previously identified rodent paramyxovirus-related viruses. Our findings suggest the circulation of previously unknown paramyxoviruses in African rodents and shrews, and provide new information regarding the geographical distribution and genetic diversity of paramyxoviruses.

  5. Molecular characterisation of Atlantic salmon paramyxovirus (ASPV): A novel paramyxovirus associated with proliferative gill inflammation

    Science.gov (United States)

    Falk, K.; Batts, W.N.; Kvellestad, A.; Kurath, G.; Wiik-Nielsen, J.; Winton, J.R.

    2008-01-01

    Atlantic salmon paramyxovirus (ASPV) was isolated in 1995 from gills of farmed Atlantic salmon suffering from proliferative gill inflammation. The complete genome sequence of ASPV was determined, revealing a genome 16,968 nucleotides in length consisting of six non-overlapping genes coding for the nucleo- (N), phospho- (P), matrix- (M), fusion- (F), haemagglutinin-neuraminidase- (HN) and large polymerase (L) proteins in the order 3???-N-P-M-F-HN-L-5???. The various conserved features related to virus replication found in most paramyxoviruses were also found in ASPV. These include: conserved and complementary leader and trailer sequences, tri-nucleotide intergenic regions and highly conserved transcription start and stop signal sequences. The P gene expression strategy of ASPV was like that of the respiro-, morbilli- and henipaviruses, which express the P and C proteins from the primary transcript and edit a portion of the mRNA to encode V and W proteins. Sequence similarities among various features related to virus replication, pairwise comparisons of all deduced ASPV protein sequences with homologous regions from other members of the family Paramyxoviridae, and phylogenetic analyses of these amino acid sequences suggested that ASPV was a novel member of the sub-family Paramyxovirinae, most closely related to the respiroviruses. ?? 2008 Elsevier B.V. All rights reserved.

  6. Paramyxoviruses in reptiles: a review.

    Science.gov (United States)

    Hyndman, Timothy H; Shilton, Cathy M; Marschang, Rachel E

    2013-08-30

    In 1972, an outbreak of neurorespiratory disease in a Swiss serpentarium formed the basis for the first description of a paramyxovirus isolated from a reptile. In the forty years since this outbreak, there have been over 50 published reports about reptilian paramyxoviruses from all over the world. The majority of these investigations have concerned themselves with ferlaviruses (sometimes previously referred to as ophidian paramyxoviruses, or OPMV). The biology of these viruses is reviewed and this is followed by a review of the clinical findings that are associated with ferlaviral infection and the various diagnostic tests that are used to identify infected reptiles. Recently, a second, and highly divergent, reptilian paramyxovirus, Sunshine virus, was described in Australian pythons, so it is an opportune time to reflect on the paramyxoviruses that infect reptiles.

  7. Avian Paramyxovirus: A Brief Review.

    Science.gov (United States)

    Gogoi, P; Ganar, K; Kumar, S

    2017-02-01

    Avian paramyxoviruses (APMVs) have been reported from a wide variety of avian species around the world. Avian paramyxoviruses are economically significant because of the huge mortality and morbidity associated with it. Twelve different serotypes of APMV have been reported till date. Avian paramyxoviruses belong to the family Paramyxoviridae under genus Avulavirus. Newcastle disease virus (APMV-1) is the most characterized members among the APMV serotypes. Complete genome sequence of all twelve APMV serotypes has been published recently. In recent years, APMV-1 has attracted the virologists for its oncolytic activity and its use as a vaccine vector for both animals and humans. The recombinant APMV-based vaccine offers a pertinent choice for the construction of live attenuated vaccine due to its minimum recombination frequency, modular nature of transcription and lack of DNA phase during its replication. Although insufficient data are available regarding other APMV serotypes, our understanding about the APMV biology is expanding rapidly because of the availability of modern molecular biology tools and high-throughput complete genome sequencing.

  8. Newcastle Disease Virus and Other Avian Paramyxoviruses

    Science.gov (United States)

    There are currently 11 recognized serotypes of avian paramyxovirus. Type 1 is the most important for poultry and includes Newcastle disease virus (NDV), which is a form of avian paramyxovirus type 1 (APMV-1) that is highly virulent for chickens and turkeys. NDV is considered to be one of the mos...

  9. Characterization of pigeon paramyxoviruses (Newcastle disease virus isolated in South Africa from 2001 to 2006

    Directory of Open Access Journals (Sweden)

    C. Abolnik

    2008-08-01

    Full Text Available Pigeon paramyxovirus type 1 (PPMV-1, a variant of Newcastle disease virus that primarily affects doves and pigeons has been isolated in South Africa since the mid-1980s. Phylogenetic evidence indicates that pigeon paramyxovirus type 1 viruses were introduced in to South Africa on multiple occasions, based on the presence of two separate lineages, 4bi and 4bii, that have been circulating in Europe and the Far East since the early 1990s. During 2006, a PPMV-1 virus was isolated from an African ground hornbil(l Bucorvus leadbeateri which becamea cutely infected with PPMV-1 and died, probably after scavenging off infected dove carcasses in the region, since a closely-related PPMV-1 strain was also isolated from doves collected nearby. The hornbill isolate had lCPl and MDT values characteristic of PPMV-1s trains. The threat of PPMV-1 to poultry production and biodiversity in southern Africa highlights the importance of monitoring the spread of this strain.

  10. Structure and assembly of a paramyxovirus matrix protein.

    Science.gov (United States)

    Battisti, Anthony J; Meng, Geng; Winkler, Dennis C; McGinnes, Lori W; Plevka, Pavel; Steven, Alasdair C; Morrison, Trudy G; Rossmann, Michael G

    2012-08-28

    Many pleomorphic, lipid-enveloped viruses encode matrix proteins that direct their assembly and budding, but the mechanism of this process is unclear. We have combined X-ray crystallography and cryoelectron tomography to show that the matrix protein of Newcastle disease virus, a paramyxovirus and relative of measles virus, forms dimers that assemble into pseudotetrameric arrays that generate the membrane curvature necessary for virus budding. We show that the glycoproteins are anchored in the gaps between the matrix proteins and that the helical nucleocapsids are associated in register with the matrix arrays. About 90% of virions lack matrix arrays, suggesting that, in agreement with previous biological observations, the matrix protein needs to dissociate from the viral membrane during maturation, as is required for fusion and release of the nucleocapsid into the host's cytoplasm. Structure and sequence conservation imply that other paramyxovirus matrix proteins function similarly.

  11. Pooling ASR data for closely related languages

    CSIR Research Space (South Africa)

    Van Heerden, C

    2010-05-01

    Full Text Available We describe several experiments that were conducted to assess the viability of data pooling as a means to improve speech-recognition performance for under-resourced languages. Two groups of closely related languages from the Southern Bantu language...

  12. The Paramyxovirus Polymerase Complex as a Target for Next-Generation Anti-Paramyxovirus Therapeutics

    Directory of Open Access Journals (Sweden)

    Richard K Plemper

    2015-05-01

    Full Text Available The paramyxovirus family includes major human and animal pathogens, including measles virus, mumps virus, and human respiratory syncytial virus (RSV, as well as the emerging zoonotic Hendra and Nipah viruses. In the United States, RSV is the leading cause of infant hospitalizations due to viral infectious disease. Despite their clinical significance, effective drugs for the improved management of paramyxovirus disease are lacking. The development of novel anti-paramyxovirus therapeutics is therefore urgently needed. Paramyxoviruses contain RNA genomes of negative polarity, necessitating a virus-encoded RNA-dependent RNA polymerase (RdRp complex for replication and transcription. Since an equivalent enzymatic activity is absent in host cells, the RdRp complex represents an attractive druggable target, although structure-guided drug development campaigns are hampered by the lack of high-resolution RdRp crystal structures. Here, we review the current structural and functional insight into the paramyxovirus polymerase complex in conjunction with an evaluation of the mechanism of activity and developmental status of available experimental RdRp inhibitors. Our assessment spotlights the importance of the RdRp complex as a premier target for therapeutic intervention and examines how high-resolution insight into the organization of the complex will pave the path towards the structure-guided design and optimization of much-needed next-generation paramyxovirus RdRp blockers.

  13. Fatal systemic necrotizing infections associated with a novel paramyxovirus, anaconda paramyxovirus, in green anaconda juveniles.

    Science.gov (United States)

    Woo, Patrick C Y; Lau, Susanna K P; Martelli, Paolo; Hui, Suk-Wai; Lau, Candy C Y; Fan, Rachel Y Y; Groff, Joseph M; Tam, Emily W T; Chan, Kwok-Hung; Yuen, Kwok-Yung

    2014-10-01

    Beginning in July 2011, 31 green anaconda (Eunectes murinus) juveniles from an oceanarium in Hong Kong died over a 12-month period. Necropsy revealed at least two of the following features in 23 necropsies: dermatitis, severe pan-nephritis, and/or severe systemic multiorgan necrotizing inflammation. Histopathological examination revealed severe necrotizing inflammation in various organs, most prominently the kidneys. Electron microscopic examination of primary tissues revealed intralesional accumulations of viral nucleocapsids with diameters of 10 to 14 nm, typical of paramyxoviruses. Reverse transcription (RT)-PCR results were positive for paramyxovirus (viral loads of 2.33 × 10(4) to 1.05 × 10(8) copies/mg tissue) in specimens from anaconda juveniles that died but negative in specimens from the two anaconda juveniles and anaconda mother that survived. None of the other snakes in the park was moribund, and RT-PCR results for surveillance samples collected from other snakes were negative. The virus was isolated from BHK21 cells, causing cytopathic effects with syncytial formation. The virus could also replicate in 25 of 27 cell lines of various origins, in line with its capability for infecting various organs. Electron microscopy with cell culture material revealed enveloped virus with the typical "herringbone" appearance of helical nucleocapsids in paramyxoviruses. Complete genome sequencing of five isolates confirmed that the infections originated from the same clone. Comparative genomic and phylogenetic analyses and mRNA editing experiments revealed a novel paramyxovirus in the genus Ferlavirus, named anaconda paramyxovirus, with a typical Ferlavirus genomic organization of 3'-N-U-P/V/I-M-F-HN-L-5'. Epidemiological and genomic analyses suggested that the anaconda juveniles acquired the virus perinatally from the anaconda mother rather than from other reptiles in the park, with subsequent interanaconda juvenile transmission.

  14. Social comparison orientation as related to two types of closeness

    NARCIS (Netherlands)

    Buunk, Abraham P.; Dijkstra, Pieternel; Bosch, Zwenneke A.; Dijkstra, Arie; Barelds, Dick P. H.

    Two studies examined the relationship between social comparison orientation (SCO) and two types of closeness (dimensional closeness and psychological closeness) in the context of appearance-related comparisons among women. A pilot study showed that these two types were relatively independent

  15. Paramyxovirus activation and inhibition of innate immune responses.

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    Parks, Griffith D; Alexander-Miller, Martha A

    2013-12-13

    Paramyxoviruses represent a remarkably diverse family of enveloped nonsegmented negative-strand RNA viruses, some of which are the most ubiquitous disease-causing viruses of humans and animals. This review focuses on paramyxovirus activation of innate immune pathways, the mechanisms by which these RNA viruses counteract these pathways, and the innate response to paramyxovirus infection of dendritic cells (DC). Paramyxoviruses are potent activators of extracellular complement pathways, a first line of defense that viruses must face during natural infections. We discuss mechanisms by which these viruses activate and combat complement to delay neutralization. Once cells are infected, virus replication drives type I interferon (IFN) synthesis that has the potential to induce a large number of antiviral genes. Here we describe four approaches by which paramyxoviruses limit IFN induction: by limiting synthesis of IFN-inducing aberrant viral RNAs, through targeted inhibition of RNA sensors, by providing viral decoy substrates for cellular kinase complexes, and through direct blocking of the IFN promoter. In addition, paramyxoviruses have evolved diverse mechanisms to disrupt IFN signaling pathways. We describe three general mechanisms, including targeted proteolysis of signaling factors, sequestering cellular factors, and upregulation of cellular inhibitors. DC are exceptional cells with the capacity to generate adaptive immunity through the coupling of innate immune signals and T cell activation. We discuss the importance of innate responses in DC following paramyxovirus infection and their consequences for the ability to mount and maintain antiviral T cells.

  16. 12 CFR 225.123 - Activities closely related to banking.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Activities closely related to banking. 225.123 Section 225.123 Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) BOARD OF GOVERNORS OF THE FEDERAL... Holding Companies Interpretations § 225.123 Activities closely related to banking. (a) Effective June 15...

  17. 12 CFR 225.129 - Activities closely related to banking.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Activities closely related to banking. 225.129 Section 225.129 Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) BOARD OF GOVERNORS OF THE FEDERAL... Holding Companies Interpretations § 225.129 Activities closely related to banking. Courier activities. The...

  18. Tonal bilingualism : the case of two closely related Chinese dialects

    NARCIS (Netherlands)

    Wu, Junru

    2015-01-01

    Tonal bilinguals of two closely related Chinese dialects handle two tonal systems in their mind; their two vocabularies are from closely related dialects; and they write translation equivalents with common Chinese characters. Their unique language situation makes their mind special. This thesis inve

  19. Initiation and regulation of paramyxovirus transcription and replication.

    Science.gov (United States)

    Noton, Sarah L; Fearns, Rachel

    2015-05-01

    The paramyxovirus family has a genome consisting of a single strand of negative sense RNA. This genome acts as a template for two distinct processes: transcription to generate subgenomic, capped and polyadenylated mRNAs, and genome replication. These viruses only encode one polymerase. Thus, an intriguing question is, how does the viral polymerase initiate and become committed to either transcription or replication? By answering this we can begin to understand how these two processes are regulated. In this review article, we present recent findings from studies on the paramyxovirus, respiratory syncytial virus, which show how its polymerase is able to initiate transcription and replication from a single promoter. We discuss how these findings apply to other paramyxoviruses. Then, we examine how trans-acting proteins and promoter secondary structure might serve to regulate transcription and replication during different phases of the paramyxovirus replication cycle.

  20. Close pairs of relative equilibria for identical point vortices

    DEFF Research Database (Denmark)

    Dirksen, Tobias; Aref, Hassan

    2011-01-01

    Numerical solution of the classical problem of relative equilibria for identical point vortices on the unbounded plane reveals configurations that are very close to the analytically known, centered, symmetrically arranged, nested equilateral triangles. New numerical solutions of this kind are found...... also has this property, and new relative equilibria close to the nested, symmetrically arranged, regular heptagons have been found. The centered regular nonagon is also marginally stable. Again, a new family of close relative equilibria has been found. The closest relative equilibrium pairs occur...

  1. Competitive strategies differentiate closely related species of marine actinobacteria

    National Research Council Canada - National Science Library

    Patin, Nastassia V; Duncan, Katherine R; Dorrestein, Pieter C; Jensen, Paul R

    2016-01-01

    ... to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies...

  2. Evidence for a new avian paramyxovirus serotype-10 detected in Rockhopper penguins from the Falkland Islands

    Science.gov (United States)

    The biological, serological and genomic characterization of a paramyxovirus recently isolated from rockhopper penguins (Eudyptes chrysocome) suggested that this virus represented a new avian paramyxovirus group, APMV10. This penguin virus resembled other APMV by electron microscopy; however, its vi...

  3. Sexual disclosures: connections to relational satisfaction and closeness.

    Science.gov (United States)

    Coffelt, Tina A; Hess, Jon A

    2014-01-01

    This study examines sexual communication by describing the content of sexual disclosures within marital relationships and assessing the association between sexual disclosures and relational outcomes, specifically relational satisfaction and closeness. A survey administered to 293 married individuals (58% female) who had an average age of 40 years (range = 20-73), 13.7 years of marriage (range = 1 month to 54 years), and who reported high levels of relational satisfaction assessed the relation between the content of sexual disclosures and satisfaction and closeness. While sexual disclosures are made infrequently, positive affect and sexual preferences are disclosed more than negative topics and disclosing sexual information is positively related to relationship satisfaction, rρ(280) =.26, p sexual information and relationship satisfaction and closeness, as reported by individuals experiencing relationship satisfaction.

  4. Discovery of new feline paramyxoviruses in domestic cats with chronic kidney disease

    NARCIS (Netherlands)

    Sieg, Michael; Heenemann, Kristin; Rückner, Antje; Burgener, Iwan; Oechtering, Gerhard; Vahlenkamp, Thomas W

    2015-01-01

    Paramyxoviruses constitute a large family of enveloped RNA viruses including important pathogens in veterinary and human medicine. Recently, feline paramyxoviruses, genus morbillivirus, were detected in cats from Hong Kong and Japan. Here we describe the discovery of several new feline paramyxovirus

  5. Differentiation of closely related fungi by electronic nose analysis

    DEFF Research Database (Denmark)

    Karlshøj, Kristian; Nielsen, Per Væggemose; Larsen, Thomas Ostenfeld

    2007-01-01

    In this work the potential of electronic nose analysis for differentiation of closely related fun has been described. A total of 20 isolates of the cheese-associated species Geotrichum candidum, Penicillium camemberti, P.nordicum, and Proqueford and its closely related species P paneum, P carneum...... as well as the noacheese ociated P. expansum have been investigated by electronic nose, GC-MS, and LGMS analysis. The isolates were inoculated on yeast extract sucroseagar in 20-mL headspace flasks and electronicnose analysis was performed daily for a-74period. To assess which volatile metabolites...... by high pressure liquid chromatography, coupled-to a diode array detector and a time of flight mass spectrometer. Several mycotoxins were detected in samples from the specles P.nordicum, P.roqueforti, P.paneum, P.carneum, and P.expansum. Differentiation of closely related mycotoxin producing fungi...

  6. Comparative Genomics via Wavelet Analysis for Closely Related Bacteria

    Directory of Open Access Journals (Sweden)

    Jiuzhou Song

    2004-01-01

    Full Text Available Comparative genomics has been a valuable method for extracting and extrapolating genome information among closely related bacteria. The efficiency of the traditional methods is extremely influenced by the software method used. To overcome the problem here, we propose using wavelet analysis to perform comparative genomics. First, global comparison using wavelet analysis gives the difference at a quantitative level. Then local comparison using keto-excess or purine-excess plots shows precise positions of inversions, translocations, and horizontally transferred DNA fragments. We firstly found that the level of energy spectra difference is related to the similarity of bacteria strains; it could be a quantitative index to describe the similarities of genomes. The strategy is described in detail by comparisons of closely related strains: S.typhi CT18, S.typhi Ty2, S.typhimurium LT2, H.pylori 26695, and H.pylori J99.

  7. Comparative Genomics via Wavelet Analysis for Closely Related Bacteria

    Science.gov (United States)

    Song, Jiuzhou; Ware, Tony; Liu, Shu-Lin; Surette, M.

    2004-12-01

    Comparative genomics has been a valuable method for extracting and extrapolating genome information among closely related bacteria. The efficiency of the traditional methods is extremely influenced by the software method used. To overcome the problem here, we propose using wavelet analysis to perform comparative genomics. First, global comparison using wavelet analysis gives the difference at a quantitative level. Then local comparison using keto-excess or purine-excess plots shows precise positions of inversions, translocations, and horizontally transferred DNA fragments. We firstly found that the level of energy spectra difference is related to the similarity of bacteria strains; it could be a quantitative index to describe the similarities of genomes. The strategy is described in detail by comparisons of closely related strains: S.typhi CT18, S.typhi Ty2, S.typhimurium LT2, H.pylori 26695, and H.pylori J99.

  8. Structural and mechanistic studies of measles virus illuminate paramyxovirus entry.

    Directory of Open Access Journals (Sweden)

    Richard K Plemper

    2011-06-01

    Full Text Available Measles virus (MeV, a member of the paramyxovirus family of enveloped RNA viruses and one of the most infectious viral pathogens identified, accounts for major pediatric morbidity and mortality worldwide although coordinated efforts to achieve global measles control are in place. Target cell entry is mediated by two viral envelope glycoproteins, the attachment (H and fusion (F proteins, which form a complex that achieves merger of the envelope with target cell membranes. Despite continually expanding knowledge of the entry strategies employed by enveloped viruses, our molecular insight into the organization of functional paramyxovirus fusion complexes and the mechanisms by which the receptor binding by the attachment protein triggers the required conformational rearrangements of the fusion protein remain incomplete. Recently reported crystal structures of the MeV attachment protein in complex with its cellular receptors CD46 or SLAM and newly developed functional assays have now illuminated some of the fundamental principles that govern cell entry by this archetype member of the paramyxovirus family. Here, we review these advances in our molecular understanding of MeV entry in the context of diverse entry strategies employed by other members of the paramyxovirus family.

  9. Rations of Closely Related Elements in Soil and Their Inplications

    Institute of Scientific and Technical Information of China (English)

    XINGGUANG-XI; HOUWEN-HUA; 等

    1991-01-01

    This paper has investigated the ratios of closely related elements such as Mn,Cr,V,Ni,Co,Cu,Pb,Cd,Ba,Sr,La and Ce in the major soils of China,and the factors affecting them,and explored their use as indicators in soil formation,material transport and environmental pollution.Results show that the effect of soil-forming processes on the ratios of closely related elements varied with different elements,and became greater in the sequence of Ce/La grassland soils>desert soils and increasing gradually from the semi-arid subhumid zone soils>the temperate zone neutral soils>the north subtropic zone soils>tropical and subtropical acid soils.

  10. Antigenicity and Hemaglutination Activity of a Recombinant Hemagglutinin-Neuraminidase of Paramyxovirus Tianjin Strain

    Institute of Scientific and Technical Information of China (English)

    Mei LI; Li-jun YUAN; Li-ying SHI; Xiao-mian LI; Qing WANG; Wen-xiu WANG

    2008-01-01

    Paramyxovirus Tianjin strain, a new genotype of Sendal virus, was isolated from the lungs of common cotton-eared marmoset that died of severe respiratory infection in the marmoset colonies. The 19.28% IgM positive rate in the young children with acute respiratory tract infection suggested a close relationship between Tianjin strain and humans. Hemagglutinin-neuraminidase (HN) is its major transmembrane glycoprotein responsible for viral attachment, penetration and release. To clear the relationship between HN structure and function of paramyxovirus Tianjin strain, rHN1, rHN2 and rHN3 overlapping the ectodomain of HN protein were expressed. Their antigenicity and hemaglutination activity, as well as cross reactivity to standard antisera against influenza virus type A, type B were analyzed. The results indicated expressed rHNs have the natural antigenicity.The segment rHN2 possesses more linear epitopes exposed on the surface of the native I-IN protein than found in segments rHN3 and rHN1. The hemagglutination activity of segment rHN3 is higher than that of segments rHN2 and rHN1, and partially dependent on the three-dimensional conformation of HN3 protein. Cross-reactivity between rHNs and standard antisera against influenza virus type A, type B suggested that rHNs might not be the best alternative as specific antigens to detect virus in clinicalserum specimens.

  11. Experimental avian paramyxovirus serotype-3 infection in chickens and turkeys.

    Science.gov (United States)

    Kumar, Sachin; Militino Dias, Flavia; Nayak, Baibaswata; Collins, Peter L; Samal, Siba K

    2010-01-01

    Avian paramyxoviruses (APMV) are divided into nine serotypes. Newcastle disease virus (APMV-1) is the most extensively characterized, while relatively little information is available for the other APMV serotypes. In the present study, we examined the pathogenicity of two divergent strains of APMV-3, Netherlands and Wisconsin, in (i) 9-day-old embryonated chicken eggs, (ii) 1-day-old specific pathogen free (SPF) chicks and turkeys, and (iii) 2-week-old SPF chickens and turkeys. The mean death time in 9-day-old embryonated chicken eggs was 112 h for APMV-3 strain Netherlands and > 168 h for strain Wisconsin. The intracerebral pathogenicity index in 1-day-old chicks for strain Netherlands was 0.39 and for strain Wisconsin was zero. Thus, both strains are lentogenic. Both the strains replicated well in brain tissue when inoculated intracerebrally in 1-day-old SPF chicks, but without causing death. Mild respiratory disease signs were observed in 1-day-old chickens and turkeys when inoculated through oculonasal route with either strain. There were no overt signs of illness in 2-weeks-old chickens and turkeys by either strain, although all the birds seroconverted after infection. The viruses were isolated predominantly from brain, lungs, spleens, trachea, pancreas and kidney. Immunohistochemistry studies also showed the presence of large amount of viral antigens in both epithelial and sub-epithelial lining of respiratory and alimentary tracts. Our result suggests systemic spread of APMV-3 even though the viral fusion glycoprotein does not contain the canonical furin proteases cleavage site. Furthermore, there was little or no disease despite systemic viral spread and abundant viral replication in all the tissues tested.

  12. Extracted facial feature of racial closely related faces

    Science.gov (United States)

    Liewchavalit, Chalothorn; Akiba, Masakazu; Kanno, Tsuneo; Nagao, Tomoharu

    2010-02-01

    Human faces contain a lot of demographic information such as identity, gender, age, race and emotion. Human being can perceive these pieces of information and use it as an important clue in social interaction with other people. Race perception is considered the most delicacy and sensitive parts of face perception. There are many research concerning image-base race recognition, but most of them are focus on major race group such as Caucasoid, Negroid and Mongoloid. This paper focuses on how people classify race of the racial closely related group. As a sample of racial closely related group, we choose Japanese and Thai face to represents difference between Northern and Southern Mongoloid. Three psychological experiment was performed to study the strategies of face perception on race classification. As a result of psychological experiment, it can be suggested that race perception is an ability that can be learn. Eyes and eyebrows are the most attention point and eyes is a significant factor in race perception. The Principal Component Analysis (PCA) was performed to extract facial features of sample race group. Extracted race features of texture and shape were used to synthesize faces. As the result, it can be suggested that racial feature is rely on detailed texture rather than shape feature. This research is a indispensable important fundamental research on the race perception which are essential in the establishment of human-like race recognition system.

  13. MHC adaptive divergence between closely related and sympatric African cichlids.

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    Jonatan Blais

    Full Text Available BACKGROUND: The haplochromine cichlid species assemblages of Lake Malawi and Victoria represent some of the most important study systems in evolutionary biology. Identifying adaptive divergence between closely-related species can provide important insights into the processes that may have contributed to these spectacular radiations. Here, we studied a pair of sympatric Lake Malawi species, Pseudotropheus fainzilberi and P. emmiltos, whose reproductive isolation depends on olfactory communication. We tested the hypothesis that these species have undergone divergent selection at MHC class II genes, which are known to contribute to olfactory-based mate choice in other taxa. METHODOLOGY/PRINCIPAL FINDINGS: Divergent selection on functional alleles was inferred from the higher genetic divergence at putative antigen binding sites (ABS amino acid sequences than at putatively neutrally evolving sites at intron 1, exon 2 synonymous sequences and exon 2 amino acid residues outside the putative ABS. In addition, sympatric populations of these fish species differed significantly in communities of eukaryotic parasites. CONCLUSIONS/SIGNIFICANCE: We propose that local host-parasite coevolutionary dynamics may have driven adaptive divergence in MHC alleles, influencing odor-mediated mate choice and leading to reproductive isolation. These results provide the first evidence for a novel mechanism of adaptive speciation and the first evidence of adaptive divergence at the MHC in closely related African cichlid fishes.

  14. eShadow: A tool for comparing closely related sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ovcharenko, Ivan; Boffelli, Dario; Loots, Gabriela G.

    2004-01-15

    Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing, has been pioneered for predicting functional elements in the human genome through the analysis of multiple primate sequence alignments. We have expanded this theoretical approach to create a computational tool, eShadow, for the identification of elements under selective pressure in multiple sequence alignments of closely related genomes, such as in comparisons of human to primate or mouse to rat DNA. This tool integrates two different statistical methods and allows for the dynamic visualization of the resulting conservation profile. eShadow also includes a versatile optimization module capable of training the underlying Hidden Markov Model to differentially predict functional sequences. This module grants the tool high flexibility in the analysis of multiple sequence alignments and in comparing sequences with different divergence rates. Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements. The eShadow tool is publicly available at http://eshadow.dcode.org/

  15. Climate-induced range overlap among closely related species

    Science.gov (United States)

    Krosby, Meade; Wilsey, Chad B.; McGuire, Jenny L.; Duggan, Jennifer M.; Nogeire, Theresa M.; Heinrichs, Julie A.; Tewksbury, Joshua J.; Lawler, Joshua J.

    2015-09-01

    Contemporary climate change is causing large shifts in biotic distributions, which has the potential to bring previously isolated, closely related species into contact. This has led to concern that hybridization and competition could threaten species persistence. Here, we use bioclimatic models to show that future range overlap by the end of the century is predicted for only 6.4% of isolated, congeneric species pairs of New World birds, mammals and amphibians. Projected rates of climate-induced overlap are higher for birds (11.6%) than for mammals (4.4%) or amphibians (3.6%). As many species will have difficulty tracking shifting climates, actual rates of future overlap are likely to be far lower, suggesting that hybridization and competition impacts may be relatively modest.

  16. Detecting Horizontal Gene Transfer between Closely Related Taxa.

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    Orit Adato

    2015-10-01

    Full Text Available Horizontal gene transfer (HGT, the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically derived genes in its recipient genome. Detecting HGT between closely related species or strains is challenging, as the phylogenetic signal is usually weak and the nucleotide composition is normally nearly identical. Nevertheless, there is a great importance in detecting HGT between congeneric species or strains, especially in clinical microbiology, where understanding the emergence of new virulent and drug-resistant strains is crucial, and often time-sensitive. We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM. Using CRM, the algorithm assigns a confidence score based on "unusual" sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set. When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain.

  17. Unity in diversity: shared mechanism of entry among paramyxoviruses.

    Science.gov (United States)

    Palgen, Jean-Louis; Jurgens, Eric M; Moscona, Anne; Porotto, Matteo; Palermo, Laura M

    2015-01-01

    The Paramyxoviridae family includes many viruses that are pathogenic in humans, including parainfluenza viruses, measles virus, respiratory syncytial virus, and the emerging zoonotic Henipaviruses. No effective treatments are currently available for these viruses, and there is a need for efficient antiviral therapies. Paramyxoviruses enter the target cell by binding to a cell surface receptor and then fusing the viral envelope with the target cell membrane, allowing the release of the viral genome into the cytoplasm. Blockage of these crucial steps prevents infection and disease. Binding and fusion are driven by two virus-encoded glycoproteins, the receptor-binding protein and the fusion protein, that together form the viral "fusion machinery." The development of efficient antiviral drugs requires a deeper understanding of the mechanism of action of the Paramyxoviridae fusion machinery, which is still controversial. Here, we review recent structural and functional data on these proteins and the current understanding of the mechanism of the paramyxovirus cell entry process.

  18. Avian paramyxoviruses serotype 3 isolated from captive birds in Israel: clinical signs, pathology, and antigenic characterization.

    Science.gov (United States)

    Shihmanter, E; Weisman, Y; Lublin, A; Mechani, S; Gruenberg, R; Horowith, H; Lipkind, M

    1998-01-01

    Thirteen HA agents were isolated in Israel from captive flamingoes (Phoenicopterus ruber), Egyptian geese (Alopochen aegyptiacus) belonging to order Anseriformes, and ibis (Guara rubra) belonging to order Ciconiiformes. The isolation was done from postmortem materials in three cases of severe respiratory disease with high mortality. The isolates were examined serologically and identified as belonging to the serotype 3 of avian paramyxoviruses (APMV-3). The isolates were more close antigenically to the APMV-3b variety (prototype strain--APMV-3/Parakeet/Netherlands/449/75) than to the APMV-3a variety (prototype strain--APMV-3/Turkey/Wisconsin/68). This is the first isolation of APMV-3 from birds belonging to the orders Anseriformes and Ciconiiformes.

  19. Competitive strategies differentiate closely related species of marine actinobacteria.

    Science.gov (United States)

    Patin, Nastassia V; Duncan, Katherine R; Dorrestein, Pieter C; Jensen, Paul R

    2016-02-01

    Although competition, niche partitioning, and spatial isolation have been used to describe the ecology and evolution of macro-organisms, it is less clear to what extent these principles account for the extraordinary levels of bacterial diversity observed in nature. Ecological interactions among bacteria are particularly challenging to address due to methodological limitations and uncertainties over how to recognize fundamental units of diversity and link them to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies. Using a direct challenge assay to investigate inhibitory interactions with members of the bacterial community, we observed a temporal difference in the onset of inhibition. The majority of inhibitory activity exhibited by Salinispora arenicola occurred early in its growth cycle and was linked to antibiotic production. In contrast, most inhibition by Salinispora tropica occurred later in the growth cycle and was more commonly linked to nutrient depletion or other sources. Comparative genomics support these differences, with S. arenicola containing nearly twice the number of secondary metabolite biosynthetic gene clusters as S. tropica, indicating a greater potential for secondary metabolite production. In contrast, S. tropica is enriched in gene clusters associated with the acquisition of growth-limiting nutrients such as iron. Coupled with differences in growth rates, the results reveal that S. arenicola uses interference competition at the expense of growth, whereas S. tropica preferentially employs a strategy of exploitation competition. The results support the ecological divergence of two co-occurring and closely related species of marine bacteria by providing evidence they have evolved fundamentally different strategies to compete in marine sediments.

  20. Evolution of transcriptional regulation in closely related bacteria

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    Tsoy Olga V

    2012-10-01

    Full Text Available Abstract Background The exponential growth of the number of fully sequenced genomes at varying taxonomic closeness allows one to characterize transcriptional regulation using comparative-genomics analysis instead of time-consuming experimental methods. A transcriptional regulatory unit consists of a transcription factor, its binding site and a regulated gene. These units constitute a graph which contains so-called “network motifs”, subgraphs of a given structure. Here we consider genomes of closely related Enterobacteriales and estimate the fraction of conserved network motifs and sites as well as positions under selection in various types of non-coding regions. Results Using a newly developed technique, we found that the highest fraction of positions under selection, approximately 50%, was observed in synvergon spacers (between consecutive genes from the same strand, followed by ~45% in divergon spacers (common 5’-regions, and ~10% in convergon spacers (common 3’-regions. The fraction of selected positions in functional regions was higher, 60% in transcription factor-binding sites and ~45% in terminators and promoters. Small, but significant differences were observed between Escherichia coli and Salmonella enterica. This fraction is similar to the one observed in eukaryotes. The conservation of binding sites demonstrated some differences between types of regulatory units. In E. coli, strains the interactions of the type “local transcriptional factor gene” turned out to be more conserved in feed-forward loops (FFLs compared to non-motif interactions. The coherent FFLs tend to be less conserved than the incoherent FFLs. A natural explanation is that the former imply functional redundancy. Conclusions A naïve hypothesis that FFL would be highly conserved turned out to be not entirely true: its conservation depends on its status in the transcriptional network and also from its usage. The fraction of positions under selection in

  1. Elucidation of operon structures across closely related bacterial genomes.

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    Chuan Zhou

    Full Text Available About half of the protein-coding genes in prokaryotic genomes are organized into operons to facilitate co-regulation during transcription. With the evolution of genomes, operon structures are undergoing changes which could coordinate diverse gene expression patterns in response to various stimuli during the life cycle of a bacterial cell. Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes. In the constructed graph, each node represents one orthologous gene group (OGG and a pair of nodes will be connected if any two genes, from the corresponding two OGGs respectively, are located in the same operon as immediate neighbors in any of the considered genomes. Through identifying the connected components in the above graph, we found that genes in a connected component are likely to be functionally related and these identified components tend to form treelike topology, such as paths and stars, corresponding to different biological mechanisms in transcriptional regulation as follows. Specifically, (i a path-structure component integrates genes encoding a protein complex, such as ribosome; and (ii a star-structure component not only groups related genes together, but also reflects the key functional roles of the central node of this component, such as the ABC transporter with a transporter permease and substrate-binding proteins surrounding it. Most interestingly, the genes from organisms with highly diverse living environments, i.e., biomass degraders and animal pathogens of clostridia in our study, can be clearly classified into different topological groups on some connected components.

  2. Elucidation of operon structures across closely related bacterial genomes.

    Science.gov (United States)

    Zhou, Chuan; Ma, Qin; Li, Guojun

    2014-01-01

    About half of the protein-coding genes in prokaryotic genomes are organized into operons to facilitate co-regulation during transcription. With the evolution of genomes, operon structures are undergoing changes which could coordinate diverse gene expression patterns in response to various stimuli during the life cycle of a bacterial cell. Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes. In the constructed graph, each node represents one orthologous gene group (OGG) and a pair of nodes will be connected if any two genes, from the corresponding two OGGs respectively, are located in the same operon as immediate neighbors in any of the considered genomes. Through identifying the connected components in the above graph, we found that genes in a connected component are likely to be functionally related and these identified components tend to form treelike topology, such as paths and stars, corresponding to different biological mechanisms in transcriptional regulation as follows. Specifically, (i) a path-structure component integrates genes encoding a protein complex, such as ribosome; and (ii) a star-structure component not only groups related genes together, but also reflects the key functional roles of the central node of this component, such as the ABC transporter with a transporter permease and substrate-binding proteins surrounding it. Most interestingly, the genes from organisms with highly diverse living environments, i.e., biomass degraders and animal pathogens of clostridia in our study, can be clearly classified into different topological groups on some connected components.

  3. Regulated aggregative multicellularity in a close unicellular relative of metazoa

    Science.gov (United States)

    Sebé-Pedrós, Arnau; Irimia, Manuel; del Campo, Javier; Parra-Acero, Helena; Russ, Carsten; Nusbaum, Chad; Blencowe, Benjamin J; Ruiz-Trillo, Iñaki

    2013-01-01

    The evolution of metazoans from their unicellular ancestors was one of the most important events in the history of life. However, the cellular and genetic changes that ultimately led to the evolution of multicellularity are not known. In this study, we describe an aggregative multicellular stage in the protist Capsaspora owczarzaki, a close unicellular relative of metazoans. Remarkably, transition to the aggregative stage is associated with significant upregulation of orthologs of genes known to establish multicellularity and tissue architecture in metazoans. We further observe transitions in regulated alternative splicing during the C. owczarzaki life cycle, including the deployment of an exon network associated with signaling, a feature of splicing regulation so far only observed in metazoans. Our results reveal the existence of a highly regulated aggregative stage in C. owczarzaki and further suggest that features of aggregative behavior in an ancestral protist may had been co-opted to develop some multicellular properties currently seen in metazoans. DOI: http://dx.doi.org/10.7554/eLife.01287.001 PMID:24368732

  4. Retrotranspositions in orthologous regions of closely related grass species

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    Swigoňová Zuzana

    2006-08-01

    Full Text Available Abstract Background Retrotransposons are commonly occurring eukaryotic transposable elements (TEs. Among these, long terminal repeat (LTR retrotransposons are the most abundant TEs and can comprise 50–90% of the genome in higher plants. By comparing the orthologous chromosomal regions of closely related species, the effects of TEs on the evolution of plant genomes can be studied in detail. Results Here, we compared the composition and organization of TEs within five orthologous chromosomal regions among three grass species: maize, sorghum, and rice. We identified a total of 132 full or fragmented LTR retrotransposons in these regions. As a percentage of the total cumulative sequence in each species, LTR retrotransposons occupy 45.1% of the maize, 21.1% of the rice, and 3.7% of the sorghum regions. The most common elements in the maize retrotransposon-rich regions are the copia-like retrotransposons with 39% and the gypsy-like retrotransposons with 37%. Using the contiguous sequence of the orthologous regions, we detected 108 retrotransposons with intact target duplication sites and both LTR termini. Here, we show that 74% of these elements inserted into their host genome less than 1 million years ago and that many retroelements expanded in size by the insertion of other sequences. These inserts were predominantly other retroelements, however, several of them were also fragmented genes. Unforeseen was the finding of intact genes embedded within LTR retrotransposons. Conclusion Although the abundance of retroelements between maize and rice is consistent with their different genome sizes of 2,364 and 389 Mb respectively, the content of retrotransposons in sorghum (790 Mb is surprisingly low. In all three species, retrotransposition is a very recent activity relative to their speciation. While it was known that genes re-insert into non-orthologous positions of plant genomes, they appear to re-insert also within retrotransposons, potentially

  5. Genetic diversity and mutation of avian paramyxovirus serotype 1 (Newcastle disease virus) in wild birds and evidence for intercontinental spread

    Science.gov (United States)

    Ramey, Andy M.; Reeves, Andrew B.; Ogawa, Haruko; Ip, Hon S.; Imai, Kunitoshi; Bui, V. N.; Yamaguchi, Emi; Silko, N. Y.; Afonso, C.L.

    2013-01-01

    Avian paramyxovirus serotype 1 (APMV-1), or Newcastle disease virus, is the causative agent of Newcastle disease, one of the most economically important diseases for poultry production worldwide and a cause of periodic epizootics in wild birds in North America. In this study, we examined the genetic diversity of APMV-1 isolated from migratory birds sampled in Alaska, Japan, and Russia and assessed the evidence for intercontinental virus spread using phylogenetic methods. Additionally, we predicted viral virulence using deduced amino acid residues for the fusion protein cleavage site and estimated mutation rates for the fusion gene of class I and class II migratory bird isolates. All 73 isolates sequenced as part of this study were most closely related to virus genotypes previously reported for wild birds; however, five class II genotype I isolates formed a monophyletic clade exhibiting previously unreported genetic diversity, which met criteria for the designation of a new sub-genotype. Phylogenetic analysis of wild-bird isolates provided evidence for intercontinental virus spread, specifically viral lineages of APMV-1 class II genotype I sub-genotypes Ib and Ic. This result supports migratory bird movement as a possible mechanism for the redistribution of APMV-1. None of the predicted deduced amino acid motifs for the fusion protein cleavage site of APMV-1 strains isolated from migratory birds in Alaska, Japan, and Russia were consistent with those of previously identified virulent viruses. These data therefore provide no support for these strains contributing to the emergence of avian pathogens. The estimated mutation rates for fusion genes of class I and class II wild-bird isolates were faster than those reported previously for non-virulent APMV-1 strains. Collectively, these findings provide new insight into the diversity, spread, and evolution of APMV-1 in wild birds.

  6. Genetic diversity and mutation of avian paramyxovirus serotype 1 (Newcastle disease virus) in wild birds and evidence for intercontinental spread.

    Science.gov (United States)

    Ramey, Andrew M; Reeves, Andrew B; Ogawa, Haruko; Ip, Hon S; Imai, Kunitoshi; Bui, Vuong Nghia; Yamaguchi, Emi; Silko, Nikita Y; Afonso, Claudio L

    2013-12-01

    Avian paramyxovirus serotype 1 (APMV-1), or Newcastle disease virus, is the causative agent of Newcastle disease, one of the most economically important diseases for poultry production worldwide and a cause of periodic epizootics in wild birds in North America. In this study, we examined the genetic diversity of APMV-1 isolated from migratory birds sampled in Alaska, Japan, and Russia and assessed the evidence for intercontinental virus spread using phylogenetic methods. Additionally, we predicted viral virulence using deduced amino acid residues for the fusion protein cleavage site and estimated mutation rates for the fusion gene of class I and class II migratory bird isolates. All 73 isolates sequenced as part of this study were most closely related to virus genotypes previously reported for wild birds; however, five class II genotype I isolates formed a monophyletic clade exhibiting previously unreported genetic diversity, which met criteria for the designation of a new sub-genotype. Phylogenetic analysis of wild-bird isolates provided evidence for intercontinental virus spread, specifically viral lineages of APMV-1 class II genotype I sub-genotypes Ib and Ic. This result supports migratory bird movement as a possible mechanism for the redistribution of APMV-1. None of the predicted deduced amino acid motifs for the fusion protein cleavage site of APMV-1 strains isolated from migratory birds in Alaska, Japan, and Russia were consistent with those of previously identified virulent viruses. These data therefore provide no support for these strains contributing to the emergence of avian pathogens. The estimated mutation rates for fusion genes of class I and class II wild-bird isolates were faster than those reported previously for non-virulent APMV-1 strains. Collectively, these findings provide new insight into the diversity, spread, and evolution of APMV-1 in wild birds.

  7. The signal for clathrin-mediated endocytosis of the paramyxovirus SV5 HN protein resides at the transmembrane domain-ectodomain boundary region.

    Science.gov (United States)

    Leser, G P; Ector, K J; Ng, D T; Shaughnessy, M A; Lamb, R A

    1999-09-15

    The hemagglutinin-neuraminidase (HN) glycoprotein of the paramyxovirus SV5 is internalized from the cell surface via clathrin-coated pits. However, the cytoplasmic domain of SV5 HN does not contain a previously characterized internalization motif. A cell-surface-expressed chimeric protein (APK), consisting of the cytoplasmic tail, transmembrane (TM) domain, and 12 residues of the ectodomain of HN joined to the cytoplasmic protein pyruvate kinase is internalized, indicating that the N-terminal region of HN contains an internalization signal. Although SV5 HN is internalized at a rate similar to that of influenza virus hemagglutinin (HA) mutant Y543, which contains a degenerate tyrosine-based signal in its cytoplasmic tail, the elimination of the majority of the HN cytoplasmic tail, or substitution of the HN TM domain with leucine residues, did not affect the rate of HN internalization. The HN protein of the closely related virus, Newcastle disease virus (NDV), is not internalized from the cell surface. Working under the usual convention that the TM domain consists of the hydrophobic residues bounded by two charged residues, analysis of internalization of mutant and chimeric NDV HN molecules indicates that the first seven SV5 HN ectodomain residues are critical for internalization of HN. A glutamic acid residue (E37) that abuts this presumptive HN TM domain/ectodomain boundary is important for SV5 HN internalization.

  8. Molecular characterization and complete genome sequence of avian paramyxovirus type 4 prototype strain duck/Hong Kong/D3/75

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    Collins Peter L

    2008-10-01

    Paramyxoviridae showed that APMV-4 is more closely related to the APMVs than to other paramyxoviruses, reinforcing the classification of all APMVs in the genus Avulavirus of the family Paramyxoviridae.

  9. Closing in on chemical bonds by opening up relativity theory.

    Science.gov (United States)

    Whitney, Cynthia K

    2008-03-01

    This paper develops a connection between the phenomenology of chemical bonding and the theory of relativity. Empirical correlations between electron numbers in atoms and chemical bond stabilities in molecules are first reviewed and extended. Quantitative chemical bond strengths are then related to ionization potentials in elements. Striking patterns in ionization potentials are revealed when the data are viewed in an element-independent way, where element-specific details are removed via an appropriate scaling law. The scale factor involved is not explained by quantum mechanics; it is revealed only when one goes back further, to the development of Einstein's special relativity theory.

  10. Use of Wild Relatives and Closely Related Species to Adapt Common Bean to Climate Change

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    James D. Kelly

    2013-05-01

    Full Text Available Common bean (Phaseolus vulgaris L. is an important legume crop worldwide. However, abiotic and biotic stress limits bean yields to <600 kg ha−1 in low-income countries. Current low yields result in food insecurity, while demands for increased yields to match the rate of population growth combined with the threat of climate change are significant. Novel and significant advances in genetic improvement using untapped genetic diversity available in crop wild relatives and closely related species must be further explored. A meeting was organized by the Global Crop Diversity Trust to consider strategies for common bean improvement. This review resulted from that meeting and considers our current understanding of the genetic resources available for common bean improvement and the progress that has been achieved thus far through introgression of genetic diversity from wild relatives of common bean, and from closely related species, including: P. acutifolius, P. coccineus, P. costaricensis and P. dumosus. Newly developed genomic tools and their potential applications are presented. A broad outline of research for use of these genetic resources for common bean improvement in a ten-year multi-disciplinary effort is presented.

  11. Centrin protein and genes in Trichomonas vaginalis and close relatives.

    Science.gov (United States)

    Brugerolle, G; Bricheux, G; Coffe, G

    2000-01-01

    Anti-centrin monoclonal antibodies 20H5 and 11B2 produced against Clamydomononas centrin decorated the group of basal bodies as well as very closely attached structures in all trichomonads studied and in the devescovinids Foaina and Devescovina. Moreover, these antibodies decorated the undulating membrane in Trichomonas vaginalis, Trichomitus batrachorum, and Tritrichomonas foetus, and the cresta in Foaina. Centrin was not demonstrated in the dividing spindle and paradesmosis. Immunogold labeling, both in pre- and post-embedding, confirmed that centrin is associated with the basal body cylinder and is a component of the nine anchoring arms between the terminal plate of flagellar bases and the plasma-membrane. Centrin is also associated with the hook-shaped fibers attached to basal bodies (F1, F3), the X-fiber, and along sigmoid fibers (F2) at the pelta-axostyle junction, which is the microtubule organizing center for pelta-axostyle microtubules. There was no labeling on the striated costa and parabasal fibers nor on microtubular pelta-axostyle, but the fibrous structure inside the undulating membrane was labeled in T. vaginalis. Two proteins of 22-20 kDa corresponding to the centrin molecular mass were recognized by immunoblotting using these antibodies in the three trichomonad species examined. By screening a T. vaginalis cDNA library with 20H5 antibody, two genes encoding identical protein sequences were found. The sequence comprises the 4 typical EF-hand Ca++-binding domains present in every known centrin. Trichomonad centrin is closer to the green algal cluster (70% identity) than to the yeast Cdc31 cluster (55% identity) or the Alveolata cluster (46% identity).

  12. Molecular relationships between closely related strains and species of nematodes

    Science.gov (United States)

    Butler, M. H.; Wall, S. M.; Luehrsen, K. R.; Fox, G. E.; Hecht, R. M.

    1981-01-01

    Electrophoretic comparisons have been made for 24 enzymes in the Bergerac and Bristol strains of Caenorhabditis elegans and the related species, Caenorhabditis briggsae. No variation was detected between the two strains of C. elegans. In contrast, the two species, C. elegans and C. briggsae exhibited electrophoretic differences in 22 of 24 enzymes. A consensus 5S rRNA sequence was determined for C. elegans and found to be identical to that from C. briggsae. By analogy with other species with relatively well established fossil records it can be inferred that the time of divergence between the two nematode species is probably in the tens of millions of years. The limited anatomical evolution during a time period in which proteins undergo extensive changes supports the hypothesis that anatomical evolution is not dependent on overall protein changes.

  13. Ethical Challenges embedded in qualitative research interviews with close relatives

    DEFF Research Database (Denmark)

    Haahr, Anita; Norlyk, Annelise; Hall, Elisabeth

    2013-01-01

    Nurse researchers engaged in qualitative interviews with patients and spouses in healthcare may often experience being in unforseen ethical dilemmas. Researchers are guided by the bioethical principles of justice, beneficence, non-maleficence respect for human rights and respect for autonomy...... through the entire research process. However, these principles are not sufficient to prepare researchers for unanticipated ethical dilemmas related to qualitative researchs interviews. We describe and discuss ethically challenging and difficult moments embedded in two cases from our own phenomenological...... interview studies. We argue that qualitative interviews involve navigation between being guided by bioethics as a researcher, being a therapist/nurse and being a fellow human being or even a friend. The researchers' premises to react to unexpected situations and act in a sound ethical manner must...

  14. Ethical challenges embedded in qualitative research interviews with close relatives.

    Science.gov (United States)

    Haahr, Anita; Norlyk, Annelise; Hall, Elisabeth Oc

    2014-02-01

    Nurse researchers engaged in qualitative interviews with patients and spouses in healthcare may often experience being in unforeseen ethical dilemmas. Researchers are guided by the bioethical principles of justice, beneficence, non-maleficence, respect for human rights and respect for autonomy through the entire research process. However, these principles are not sufficient to prepare researchers for unanticipated ethical dilemmas related to qualitative research interviews. We describe and discuss ethically challenging and difficult moments embedded in two cases from our own phenomenological interview studies. We argue that qualitative interviews involve navigation between being guided by bioethics as a researcher, being a therapist/nurse and being a fellow human being or even a friend. The researchers' premises to react to unexpected situations and act in a sound ethical manner must be enhanced, and there is a need for an increased focus on the researchers' ethical preparation and to continually address and discuss cases from their own interviews.

  15. Differential sensitivity of bat cells to infection by enveloped RNA viruses: coronaviruses, paramyxoviruses, filoviruses, and influenza viruses.

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    Markus Hoffmann

    Full Text Available Bats (Chiroptera host major human pathogenic viruses including corona-, paramyxo, rhabdo- and filoviruses. We analyzed six different cell lines from either Yinpterochiroptera (including African flying foxes and a rhinolophid bat or Yangochiroptera (genera Carollia and Tadarida for susceptibility to infection by different enveloped RNA viruses. None of the cells were sensitive to infection by transmissible gastroenteritis virus (TGEV, a porcine coronavirus, or to infection mediated by the Spike (S protein of SARS-coronavirus (SARS-CoV incorporated into pseudotypes based on vesicular stomatitis virus (VSV. The resistance to infection was overcome if cells were transfected to express the respective cellular receptor, porcine aminopeptidase N for TGEV or angiotensin-converting enzyme 2 for SARS-CoV. VSV pseudotypes containing the S proteins of two bat SARS-related CoV (Bg08 and Rp3 were unable to infect any of the six tested bat cell lines. By contrast, viral pseudotypes containing the surface protein GP of Marburg virus from the family Filoviridae infected all six cell lines though at different efficiency. Notably, all cells were sensitive to infection by two paramyxoviruses (Sendai virus and bovine respiratory syncytial virus and three influenza viruses from different subtypes. These results indicate that bat cells are more resistant to infection by coronaviruses than to infection by paramyxoviruses, filoviruses and influenza viruses. Furthermore, these results show a receptor-dependent restriction of the infection of bat cells by CoV. The implications for the isolation of coronaviruses from bats are discussed.

  16. Towards a more liveable life for close relatives of individuals diagnosed with bipolar disorder.

    Science.gov (United States)

    Rusner, Marie; Carlsson, Gunilla; Brunt, David; Nyström, Maria

    2013-04-01

    The life of close relatives of persons with bipolar disorder (BD) is associated with emotional distress, depression, and a high level of use of mental health care. Illness-related changes of their life situation endanger relationships, social life, finances, and occupational functioning. Understanding of facilitating conditions for close relatives is still a neglected research area. The aim of the present study thus was to explore what makes the life of close relatives of persons with BD more liveable. A lifeworld phenomenological approach was used. The findings reveal that keeping distance, having stability in everyday life, and strengthening equality through transparent communication are conditions that enable close relatives to influence the unpredictable and its consequences and thus make life more liveable. This implies contributions from close relatives, the person with BD, and the caring services. We propose that health-care support should not be divided in support for the patient and/or the close relatives but instead be designed as support for the 'patient and close relatives' as a unit. Professional caregivers need to take responsibility for creating intersubjective settings for the person with BD and their close relatives to share their needs and make joint plans for how to influence the illness-related life issues.

  17. 12 CFR 225.126 - Activities not closely related to banking.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Activities not closely related to banking. 225.126 Section 225.126 Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) BOARD OF GOVERNORS OF THE... Financial Holding Companies Interpretations § 225.126 Activities not closely related to banking. Pursuant to...

  18. Timing is everything: Fine-tuned molecular machines orchestrate paramyxovirus entry

    Energy Technology Data Exchange (ETDEWEB)

    Bose, Sayantan, E-mail: sayantan_bose@hms.harvard.edu [Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500 (United States); Jardetzky, Theodore S. [Department of Structural Biology and Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305 (United States); Lamb, Robert A., E-mail: ralamb@northwestern.edu [Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500 (United States); Howard Hughes Medical Institute, Northwestern University, Evanston, IL 60208-3500 (United States)

    2015-05-15

    The Paramyxoviridae include some of the great and ubiquitous disease-causing viruses of humans and animals. In most paramyxoviruses, two viral membrane glycoproteins, fusion protein (F) and receptor binding protein (HN, H or G) mediate a concerted process of recognition of host cell surface molecules followed by fusion of viral and cellular membranes, resulting in viral nucleocapsid entry into the cytoplasm. The interactions between the F and HN, H or G viral glycoproteins and host molecules are critical in determining host range, virulence and spread of these viruses. Recently, atomic structures, together with biochemical and biophysical studies, have provided major insights into how these two viral glycoproteins successfully interact with host receptors on cellular membranes and initiate the membrane fusion process to gain entry into cells. These studies highlight the conserved core mechanisms of paramyxovirus entry that provide the fundamental basis for rational anti-viral drug design and vaccine development. - Highlights: • New structural and functional insights into paramyxovirus entry mechanisms. • Current data on paramyxovirus glycoproteins suggest a core conserved entry mechanism. • Diverse mechanisms preventing premature fusion activation exist in these viruses. • Precise spacio-temporal interplay between paramyxovirus glycoproteins initiate entry.

  19. Complete Genome Sequence of the Avian Paramyxovirus Serotype 5 Strain APMV-5/budgerigar/Japan/TI/75

    Science.gov (United States)

    Hiono, Takahiro; Matsuno, Keita; Tuchiya, Kotaro; Lin, Zhifeng; Okamatsu, Masatoshi

    2016-01-01

    Here, we report the complete genome sequence of the avian paramyxovirus serotype 5 strain APMV-5/budgerigar/Japan/TI/75, which was determined using the Illumina MiSeq platform. The determined sequence shares 97% homology and similar genetic features with the previously known genome sequence of avian paramyxovirus serotype 5 strain APMV-5/budgerigar/Japan/Kunitachi/74. PMID:27660785

  20. Arterial blood pressure is closely related to ascites development in compensated HCV-related cirrhosis.

    Directory of Open Access Journals (Sweden)

    Eduardo Vilar Gomez

    Full Text Available BACKGROUND: Arterial blood pressure (BP is a reliable marker of circulatory dysfunction in cirrhotic patients. There are no prospective studies evaluating the association between different levels of arterial BP and ascites development in compensated cirrhotic patients. Therefore, we evaluated the relationship between arterial BP and ascites development in compensated cirrhotic patients. MATERIALS AND METHODS: A total of 402 patients with compensated HCV-related cirrhosis were prospectively followed during 6 years to identify ascites development. At baseline, patients underwent systolic, diastolic and mean arterial pressure (MAP measurements. Any history of arterial hypertension was also recorded. The occurrence of events such as bleeding, hepatocellular carcinoma, death and liver transplantation prior to ascites development were considered as competing risk events. RESULTS: Over a median of 156 weeks, ascites occurred in 54 patients (13%. At baseline, MAP was significantly lower in patients with ascites development (75.9 mm/Hg [95%CI, 70.3-84.3] than those without ascites (93.6 mm/Hg [95% CI: 86.6-102.3]. After adjusting for covariates, the 6-year cumulative incidence of ascites was 40% (95%CI, 34%-48% for patients with MAP<83.32 mm/Hg. In contrast, cumulative incidences of ascites were almost similar among patients with MAP values between 83.32 mm/Hg and 93.32 mm/Hg (7% [95% CI: 4%-12%], between 93.32 mm/Hg and 100.31 mm/Hg (5% [95% CI: 4%-11%] or higher than 100.31 mm/Hg (3% [95% CI: 1%-6%]. The MAP was an independent predictor of ascites development. CONCLUSIONS: The MAP is closely related to the development of ascites in compensated HCV-related cirrhosis. The risk of ascites development increases in 4.4 fold for subjects with MAP values <83.32 mm/Hg.

  1. Relationship of Dyadic Closeness with Work-Related Stress: A Daily Diary Study

    Science.gov (United States)

    Lavee, Yoav; Ben-Ari, Adital

    2007-01-01

    We examined the association between work-related stress of both spouses and daily fluctuations in their affective states and dyadic closeness. Daily diary data from 169 Israeli dual-earner couples were analyzed using multilevel modeling. The findings indicate that work stress has no direct effect on dyadic closeness but rather is mediated by the…

  2. Relationship of Dyadic Closeness with Work-Related Stress: A Daily Diary Study

    Science.gov (United States)

    Lavee, Yoav; Ben-Ari, Adital

    2007-01-01

    We examined the association between work-related stress of both spouses and daily fluctuations in their affective states and dyadic closeness. Daily diary data from 169 Israeli dual-earner couples were analyzed using multilevel modeling. The findings indicate that work stress has no direct effect on dyadic closeness but rather is mediated by the…

  3. Closely related freshwater macrophyte species, Ceratophyllum demersum and em>C. submersum, differ in temperature response

    DEFF Research Database (Denmark)

    Hyldgaard, Benita; Sorrell, Brian Keith; Brix, Hans

    2014-01-01

    1. The importance of temperature responses of photosynthesis and respiration in determining species distributions was compared in two closely related freshwater macrophytes, Ceratophyllum demersum and C. submersum. The two species differed significantly in response to temperature in the short and...

  4. Characterization of a pigeon paramyxovirus (PPMV-1 isolated from chickens in South Africa : research communication

    Directory of Open Access Journals (Sweden)

    C. Abolnik

    2004-11-01

    Full Text Available A paramyxovirus with a thermostability of 60 min (typical of velogenic viruses and a mean death time of > 90 h (typical of lentogenic viruses was isolated from layers near Mooi River, South Africa. Our results, based on comparative nucleotide sequence data indicated that the virus is pigeon paramyxovirus 1 (PPMV-1, a variant of Newcastle disease virus. The F0 cleavage site contains a 112RRKKRF117 motif, and the virus had 98 % sequence identity with PPMV-1 strains from the Far East. PPMV-1 was last reported in South Africa during the 1980s, with this being the first report of PPMV-1 isolated from chickens in South Africa.

  5. Identification and complete genome sequencing of paramyxoviruses in mallard ducks (Anas platyrhynchos using random access amplification and next generation sequencing technologies

    Directory of Open Access Journals (Sweden)

    van den Berg Thierry

    2011-10-01

    Full Text Available Abstract Background During a wildlife screening program for avian influenza A viruses (AIV and avian paramyxoviruses (APMV in Belgium, we isolated two hemagglutinating agents from pools of cloacal swabs of wild mallards (Anas platyrhynchos caught in a single sampling site at two different times. AIV and APMV1 were excluded using hemagglutination inhibition (HI testing and specific real-time RT-PCR tests. Methods To refine the virological identification of APMV2-10 realized by HI subtyping tests and in lack of validated molecular tests for APMV2-10, random access amplification was used in combination with next generation sequencing for the sequence independent identification of the viruses and the determination of their genomes. Results Three different APMVs were identified. From one pooled sample, the complete genome sequence (15054 nucleotides of an APMV4 was assembled from the random sequences. From the second pooled sample, the nearly complete genome sequence of an APMV6 (genome size of 16236 nucleotides was determined, as well as a partial sequence for an APMV4. This APMV4 was closely related but not identical to the APMV4 isolated from the first sample. Although a cross-reactivity with other APMV subtypes did not allow formal identification, the HI subtyping revealed APMV4 and APMV6 in the respective pooled samples but failed to identify the co-infecting APMV4 in the APMV6 infected pool. Conclusions These data further contribute to the knowledge about the genetic diversity within the serotypes APMV4 and 6, and confirm the limited sensitivity of the HI subtyping test. Moreover, this study demonstrates the value of a random access nucleic acid amplification method in combination with massive parallel sequencing. Using only a moderate and economical sequencing effort, the characterization and full genome sequencing of APMVs can be obtained, including the identification of viruses in mixed infections.

  6. Empathy and the expression and recognition of sarcasm by close relations or strangers.

    Science.gov (United States)

    Rockwell, Patricia

    2003-08-01

    This study examined how relational type and empathy affect the use of sarcasm. We paired interviewers of high and low empathy with either an interviewee who was closely related or a stranger. Interviewers were given 10 questions to ask the interviewee, alternating sarcastic questions with sincere questions. Following each interview, participants completed questionnaires to assess their understanding of how sarcasm affected the interview. Relationship (closely related vs stranger) was a significant factor in recognition of sarcasm but not in its use. Empathy (high vs low) did not significantly affect the production or recognition of sarcasm.

  7. Carbapenem resistance in a human clinical isolate identified to be closely related to Acinetobacter indicus.

    Science.gov (United States)

    Bonnin, Rémy A; Poirel, Laurent; van der Reijden, Tanny J K; Dijkshoorn, Lenie; Lescat, Mathilde; Nordmann, Patrice

    2014-10-01

    Here we report a case of carbapenem resistance in a human clinical isolate that was found to be closely related to the newly described environmental species Acinetobacter indicus. This strain harboured the blaOXA-23 carbapenemase gene located on a conjugative plasmid. Partial sequencing of 16S rDNA and rpoB genes, together with matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) analysis, showed that this strain was distantly related to the Acinetobacter baumannii-calcoaceticus complex and was closely related to A. indicus.

  8. 31 CFR 515.561 - Persons visiting close relatives in Cuba.

    Science.gov (United States)

    2010-07-01

    ... Cuba. 515.561 Section 515.561 Money and Finance: Treasury Regulations Relating to Money and Finance... Cuba. (a) General license. (1) Persons subject to the jurisdiction of the United States and persons... close relative, as defined in § 515.339 of this part, who is a national of Cuba, as defined in §...

  9. The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis.

    Science.gov (United States)

    Rodríguez-Ramilo, Silvia T; Wang, Jinliang

    2012-09-01

    The inference of population genetic structures is essential in many research areas in population genetics, conservation biology and evolutionary biology. Recently, unsupervised Bayesian clustering algorithms have been developed to detect a hidden population structure from genotypic data, assuming among others that individuals taken from the population are unrelated. Under this assumption, markers in a sample taken from a subpopulation can be considered to be in Hardy-Weinberg and linkage equilibrium. However, close relatives might be sampled from the same subpopulation, and consequently, might cause Hardy-Weinberg and linkage disequilibrium and thus bias a population genetic structure analysis. In this study, we used simulated and real data to investigate the impact of close relatives in a sample on Bayesian population structure analysis. We also showed that, when close relatives were identified by a pedigree reconstruction approach and removed, the accuracy of a population genetic structure analysis can be greatly improved. The results indicate that unsupervised Bayesian clustering algorithms cannot be used blindly to detect genetic structure in a sample with closely related individuals. Rather, when closely related individuals are suspected to be frequent in a sample, these individuals should be first identified and removed before conducting a population structure analysis.

  10. Identification of Avian Paramyxovirus Serotype-1 in Wild Birds in the USA

    Science.gov (United States)

    In the US, sampling for avian paramyxovirus serotype-1 (APMV-1) is generally conducted when morbidity or mortality events occur involving certain families of wild birds known to be affected by the virus, such as cormorants (Family Phalacrocoracidae), pigeons, doves (Family Columbidae), or pelicans (...

  11. Limited evidence of intercontinental dispersal of avian paramyxovirus serotype 4 by migratory birds

    Science.gov (United States)

    Avian paramyxovirus serotype 4 (APMV-4) is a single stranded RNA virus that has most often been isolated from waterfowl. Limited information has been reported regarding the prevalence, pathogenicity, and genetic diversity of AMPV-4. To assess the intercontinental dispersal of this viral agent, we se...

  12. On Enumerating Frequent Closed Patterns with Key in Multi-relational Data

    Science.gov (United States)

    Seki, Hirohisa; Honda, Yuya; Nagano, Shinya

    We study the problem of mining closed patterns in multi-relational databases. Garriga et al. (IJCAI'07) proposed an algorithm RelLCM2 for mining closed patterns (i.e., conjunctions of literals) in multi-relational data, which is an extension of LCM, an efficient enumeration algorithm for frequent closed itemsets mining proposed in the seminal paper by Uno et al. (DS'04). We assume that a database considered contains a special predicate called key (or target), which determines the entities of interest and what is to be counted. We introduce a notion of closed patterns with key (key-closedness for short), where variables in a pattern other than the one in a key predicate are considered to be existentially quantified, and they are linked to a given target object. We then define a closure operation (key-closure) for computing key-closed patterns, and show that the difference between the semantics of key-closed patterns and that of the closed patterns in RelLCM2 implies different properties of the closure operations; in particular, the uniqueness of closure does not hold for key-closure. Nevertheless, we show that we can enumerate key-closed patterns using the technique of ppc-extensions à la LCM, thereby making the enumeration possible without storage space for previously generated patterns. We also propose a literal order designed for mining key-closed patterns, which will require less search space. The correctness of our algorithm is shown, and its computational complexity is discussed. Some preliminary experimental results are also given.

  13. The effect of vaccination on the evolution and population dynamics of avian paramyxovirus-1.

    Directory of Open Access Journals (Sweden)

    Yee Ling Chong

    2010-04-01

    Full Text Available Newcastle Disease Virus (NDV is a pathogenic strain of avian paramyxovirus (aPMV-1 that is among the most serious of disease threats to the poultry industry worldwide. Viral diversity is high in aPMV-1; eight genotypes are recognized based on phylogenetic reconstruction of gene sequences. Modified live vaccines have been developed to decrease the economic losses caused by this virus. Vaccines derived from avirulent genotype II strains were developed in the 1950s and are in use globally, whereas Australian strains belonging to genotype I were developed as vaccines in the 1970s and are used mainly in Asia. In this study, we evaluated the consequences of attenuated live virus vaccination on the evolution of aPMV-1 genotypes. There was phylogenetic incongruence among trees based on individual genes and complete coding region of 54 full length aPMV-1 genomes, suggesting that recombinant sequences were present in the data set. Subsequently, five recombinant genomes were identified, four of which contained sequences from either genotype I or II. The population history of vaccine-related genotype II strains was distinct from other aPMV-1 genotypes; genotype II emerged in the late 19(th century and is evolving more slowly than other genotypes, which emerged in the 1960s. Despite vaccination efforts, genotype II viruses have experienced constant population growth to the present. In contrast, other contemporary genotypes showed population declines in the late 1990s. Additionally, genotype I and II viruses, which are circulating in the presence of homotypic vaccine pressure, have unique selection profiles compared to nonvaccine-related strains. Collectively, these data show that vaccination with live attenuated viruses has changed the evolution of aPMV-1 by maintaining a large effective population size of a vaccine-related genotype, allowing for coinfection and recombination of vaccine and wild type strains, and by applying unique selective pressures on

  14. Close monitoring as a contextual stimulator : How need for structure affects the relation between close monitoring and work outcomes

    NARCIS (Netherlands)

    Rietzschel, Eric F.; Slijkhuis, Marjette; Van Yperen, Nico W.

    2014-01-01

    In this article, we argue and demonstrate that employees' Personal Need for Structure (PNS) moderates the negative effects of close monitoring on job satisfaction, intrinsic work motivation, and innovative job performance (as rated by their supervisors). In a field study (N=295), we found that emplo

  15. Taxonomy and nomenclature of three closely related species of Eleocharis subgenus Limnochloa (Cyperaceae)

    NARCIS (Netherlands)

    Rosen, D.J.; Hatch, S.L.; Carter, R.

    2008-01-01

    A taxonomic synopsis and review of nomenclature is provided for Eleocharis cellulosa, E. mutata, and E. spiralis, three closely related species belonging to subgenus Limnochloa. One heterotypic synonym of E. mutata and the basionym and a heterotypic synonym of E. spiralis are lectotypified. The taxo

  16. Rule-based conversion of closely-related languages: a Dutch-to-Afrikaans convertor

    CSIR Research Space (South Africa)

    Van Huyssteen, GB

    2009-11-01

    Full Text Available For fast-tracking the development of resources for resource-scarce languages, one could transfer existing technologies from one language to another well-sourced, closely-related language. In this contribution, the authors describe the development...

  17. Relation between non uniform magnetic field and close binary systems period

    Directory of Open Access Journals (Sweden)

    M Zahedi

    2011-12-01

    Full Text Available  Magnetic activity of one or both components of close binary systems can cause orbital period variation of the systems.Variation in gravitational quadropole moment will change the orbital period of the systems. In this article, we suppose that magnetic field is poloidal-troidal according to dynamo theory, and finds its relation with period change in the systems.

  18. The Psychosocial Impact of Closed-Circuit Televisions on Persons with Age-Related Macular Degeneration

    Science.gov (United States)

    Huber, Jessica G.; Jutai, Jeffrey W.; Strong, J. Graham; Plotkin, Ann D.

    2008-01-01

    Closed-circuit televisions (CCTVs) are used by many elderly people who have age-related macular degeneration (AMD). The functional vision of 68 participants, which was measured immediately after they adopted CCTVs, suggested successful outcomes, but the psychosocial impact of the use of CCTVs did not peak until a month later. The findings help…

  19. Taxonomy and nomenclature of three closely related species of Eleocharis subgenus Limnochloa (Cyperaceae)

    NARCIS (Netherlands)

    Rosen, D.J.; Hatch, S.L.; Carter, R.

    2008-01-01

    A taxonomic synopsis and review of nomenclature is provided for Eleocharis cellulosa, E. mutata, and E. spiralis, three closely related species belonging to subgenus Limnochloa. One heterotypic synonym of E. mutata and the basionym and a heterotypic synonym of E. spiralis are lectotypified. The

  20. Doing Close-Relative Research: Sticking Points, Method and Ethical Considerations

    Science.gov (United States)

    Degabriele Pace, Geraldine

    2015-01-01

    Doing insider research can raise many problematic issues, particularly if the insiders are also close relatives. This paper deals with complexities arising from research which is participatory in nature. Thus, this paper seeks to describe the various sticking points that were encountered by the researcher when she decided to embark on insider…

  1. Family Communication Patterns and Relational Maintenance Behavior: Direct and Mediated Associations with Friendship Closeness

    Science.gov (United States)

    Ledbetter, Andrew M.

    2009-01-01

    In this study, both face-to-face and online relational maintenance behaviors were tested as mediators of family communication patterns and closeness with a same-sex friend. Participants included 417 young adults recruited from communication courses at a large university in the Midwestern United States. The obtained structural model demonstrated…

  2. Interspecific competition, predation, and the coexistence of three closely related neotropical armoured catfishes (Siluriformes - Callichthyidae)

    NARCIS (Netherlands)

    Mol, J.H.A.

    1995-01-01

    Tropical ecosystems are renowned for their high biodiversity with many closely related species living together. Alpha diversity of tropical freshwater fishes is also extremely high, as exemplified by the cichlid fauna of the Great African lakes and the neotropical characins. Since

  3. Interspecific competition, predation, and the coexistence of three closely related neotropical armoured catfishes (Siluriformes-Callichthyidae).

    NARCIS (Netherlands)

    Mol, J.H.A.

    1995-01-01

    Tropical ecosystems are renowned for their high biodiversity with many closely related species living together. Alpha diversity of tropical freshwater fishes is also extremely high, as exemplified by the cichlid fauna of the Great African lakes and the neotropical characins. Since Hutchinson in 1959

  4. Closely related Wolbachia recovered from different genera of Mexican Thelytokous figitidae (Hymenoptera)

    Science.gov (United States)

    Closely related novel Wolbachia strains were recovered from the thelytokous figitids Odontosema anastrephae Borgmeier and Aganaspis alujai Ovruski et al. No Wolbachia were detected in a bi-sexual strain of O. anastrephae. While the presence or absence of Wolbachia does not demonstrate that Wolbachia...

  5. Pathogenesis of two strains of avian paramyxovirus serotype 2, Yucaipa and Bangor, in chickens and turkeys.

    Science.gov (United States)

    Subbiah, Madhuri; Xiao, Sa; Khattar, Sunil K; Dias, Flavia Militino; Collins, Peter L; Samal, Siba K

    2010-09-01

    Nine serologic types of avian paramyxovirus (APMV) have been recognized. Newcastle disease virus (APMV-1) is the most extensively characterized virus, while relatively little information is available for the other APMV serotypes. In the present study, we examined the pathogenicity of two strains of APMV-2, Yucaipa and Bangor, in 9-day-old embryonated chicken eggs, 1-day-old specific-pathogen-free (SPF) chicks, and 4-wk-old SPF chickens and turkeys. The mean death time in 9-day-old embryonated chicken eggs was more than 168 hr for both strains, and their intracerebral pathogenicity index (ICPI) was zero, indicating that these viruses are nonpathogenic in chickens. When inoculated intracerebrally in 1-day-old chicks, neither strain caused disease or replicated detectably in the brain. This suggests that the zero ICPI value of APMV-2 reflects the inability of the virus to grow in neural cells. Groups of twelve 4-wk-old SPF chickens and turkeys were inoculated oculonasally with either strain, and three birds per group were euthanatized on days 2, 4, 6, and 14 postinoculation for analysis. There were no overt clinical signs of illnesses, although all birds seroconverted by day 6. The viruses were isolated predominantly from the respiratory and alimentary tracts. Immunohistochemistry studies also showed the presence of a large amount of viral antigens in epithelial linings of respiratory and alimentary tracts. There also was evidence of systemic spread even though the cleavage site of the viral fusion glycoprotein does not contain the canonical furin protease cleavage site.

  6. The Pathogenomic Sequence Analysis of B. cereus and B. Thuringiensis isolates closely related to Bacillus anthracis

    Energy Technology Data Exchange (ETDEWEB)

    Han, C S; Xie, G; Challacombe, J F; Altherr, M R; Bhotika, S S; Bruce, D; Campbell, C S; Campbell, M L; Chen, J; Chertkov, O; Cleland, C; Dimitrijevic-Bussod, M; Doggett, N A; Fawcett, J J; Glavina, T; Goodwin, L A; Hill, K K; Hitchcock, P; Jackson, P J; Keim, P; Kewalramani, A R; Longmire, J; Lucas, S; Malfatti, S; McMurry, K; Meincke, L J; Misra, M; Moseman, B L; Mundt, M; Munk, A C; Okinaka, R T; Parson-Quintana, B; Reilly, L P; Richardson, P; Robinson, D L; Rubin, E; Saunders, E; Tapia, R; Tesmer, J G; Thayer, N; Thompson, L S; Tice, H; Ticknor, L O; Wills, P L; Gilna, P; Brettin, T S

    2005-10-12

    The sequencing and analysis of two close relatives of Bacillus anthracis are reported. AFLP analysis of over 300 isolates of B. cereus, B. thuringiensis and B. anthracis identified two isolates as being very closely related to B. anthracis. One, a B. cereus, BcE33L, was isolated from a zebra carcass in Nambia; the second, a B. thuringiensis, 97-27, was isolated from a necrotic human wound. The B. cereus appears to be the closest anthracis relative sequenced to date. A core genome of over 3,900 genes was compiled for the Bacillus cereus group, including B anthracis. Comparative analysis of these two genomes with other members of the B. cereus group provides insight into the evolutionary relationships among these organisms. Evidence is presented that differential regulation modulates virulence, rather than simple acquisition of virulence factors. These genome sequences provide insight into the molecular mechanisms contributing to the host range and virulence of this group of organisms.

  7. Significant divergence of sex-related non-coding RNA expression patterns among closely related species in Drosophila

    Institute of Scientific and Technical Information of China (English)

    YANG YongFei; LI Zheng; FAN QiChang; LONG ManYuan; ZHANG WenXia

    2007-01-01

    Whether or not non-coding RNA genes play a significant role in reproductive biology and evolution of sex determination systems is an important problem. We report identification of sex-related non-coding RNA (ncRNA) genes and an analysis of ncRNAs expression patterns among Drosophila species. We detected 12 candidate ncRNAs that are expressed in the gonads of D. melanogaster by an integrative approach of RT-PCR and computational analysis of sequence conservation across species. We experimentally analyzed these ncRNA gene transcripts in head, ovary and testis of closely related species D. simulans, D. yakuba, D. pseudoobscura and D. virilis. We observed that the occurrence and extent of expression of most ncRNA fragments among closely related species show significant divergence.

  8. Angles-only relative navigation and closed-loop guidance for spacecraft proximity operations

    Science.gov (United States)

    Luo, Jianjun; Gong, Baichun; Yuan, Jianping; Zhang, Zhaofei

    2016-11-01

    This research investigates angles-only relative navigation and closed-loop guidance algorithm for spacecraft mid-range orbital proximity operations when the orbital maneuver allows for range observability. Emphasis and contribution are on developing angles-only relative navigation and guidance coupling algorithm in the context of Clohessy-Wiltshire and Tschauner-Hempel dynamics. Observability analysis of the relative state is done and the general mathematical expression of the observable condition is obtained. Coupling relationship between the angles-only relative navigation and the multi-pulse sliding guidance is discussed and its analytic expression is derived. A novel closed-loop guidance scheme is designed based on the coupling relationship and unscented kalman filter. Two-body Monte Carlo simulations are conducted to evaluate the validity and test the performance of the closed-loop system. The sensitivities of the navigation and guidance accuracy to the line-of-sight angles accuracy, initial separation and initial state uncertainties, number of pulses, and dynamics are presented and discussed.

  9. Comparative Landscape Genetics of Three Closely Related Sympatric Hesperid Butterflies with Diverging Ecological Traits

    Science.gov (United States)

    Engler, Jan O.; Balkenhol, Niko; Filz, Katharina J.; Habel, Jan C.; Rödder, Dennis

    2014-01-01

    To understand how landscape characteristics affect gene flow in species with diverging ecological traits, it is important to analyze taxonomically related sympatric species in the same landscape using identical methods. Here, we present such a comparative landscape genetic study involving three closely related Hesperid butterflies of the genus Thymelicus that represent a gradient of diverging ecological traits. We analyzed landscape effects on their gene flow by deriving inter-population connectivity estimates based on different species distribution models (SDMs), which were calculated from multiple landscape parameters. We then used SDM output maps to calculate circuit-theoretic connectivity estimates and statistically compared these estimates to actual genetic differentiation in each species. We based our inferences on two different analytical methods and two metrics of genetic differentiation. Results indicate that land use patterns influence population connectivity in the least mobile specialist T. acteon. In contrast, populations of the highly mobile generalist T. lineola were panmictic, lacking any landscape related effect on genetic differentiation. In the species with ecological traits in between those of the congeners, T. sylvestris, climate has a strong impact on inter-population connectivity. However, the relative importance of different landscape factors for connectivity varies when using different metrics of genetic differentiation in this species. Our results show that closely related species representing a gradient of ecological traits also show genetic structures and landscape genetic relationships that gradually change from a geographical macro- to micro-scale. Thus, the type and magnitude of landscape effects on gene flow can differ strongly even among closely related species inhabiting the same landscape, and depend on their relative degree of specialization. In addition, the use of different genetic differentiation metrics makes it possible to

  10. Volatiles as Chemosystematic Markers for Distinguishing Closely Related Species within the Pinus mugo Complex.

    Science.gov (United States)

    Celiński, Konrad; Bonikowski, Radosław; Wojnicka-Półtorak, Aleksandra; Chudzińska, Ewa; Maliński, Tomasz

    2015-08-01

    Headspace solid-phase microextraction (HS-SPME) coupled to GC/MS analysis was used to identify the constituents of pine-needle volatiles differentiating three closely-related pine species within the Pinus mugo complex, i.e., P. uncinata Ramond ex DC., P. uliginosa G.E.Neumann ex Wimm., and P. mugo Turra. Moreover, chemosystematic markers were proposed for the three analyzed pine species. The major constituents of the pine-needle volatiles were α-pinene (28.4%) and bornyl acetate (10.8%) for P. uncinata, δ-car-3-ene (21.5%) and α-pinene (16.1%) for P. uliginosa, and α-pinene (20%) and δ-car-3-ene (18.1%) for P. mugo. This study is the first report on the application of the composition of pine-needle volatiles for the reliable identification of closely-related pine species within the Pinus mugo complex.

  11. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.

    Science.gov (United States)

    Stefflova, Klara; Thybert, David; Wilson, Michael D; Streeter, Ian; Aleksic, Jelena; Karagianni, Panagiota; Brazma, Alvis; Adams, David J; Talianidis, Iannis; Marioni, John C; Flicek, Paul; Odom, Duncan T

    2013-08-01

    To mechanistically characterize the microevolutionary processes active in altering transcription factor (TF) binding among closely related mammals, we compared the genome-wide binding of three tissue-specific TFs that control liver gene expression in six rodents. Despite an overall fast turnover of TF binding locations between species, we identified thousands of TF regions of highly constrained TF binding intensity. Although individual mutations in bound sequence motifs can influence TF binding, most binding differences occur in the absence of nearby sequence variations. Instead, combinatorial binding was found to be significant for genetic and evolutionary stability; cobound TFs tend to disappear in concert and were sensitive to genetic knockout of partner TFs. The large, qualitative differences in genomic regions bound between closely related mammals, when contrasted with the smaller, quantitative TF binding differences among Drosophila species, illustrate how genome structure and population genetics together shape regulatory evolution.

  12. Usefulness of cpDNA markers for phylogenetic and phylogeographic analyses of closely related cactus species.

    Science.gov (United States)

    Bonatelli, I A S; Zappi, D C; Taylor, N P; Moraes, E M

    2013-02-28

    Although plastid DNA has been widely explored as a marker of choice for phylogeny and phylogeography studies, little is known about its utility for examining relationships between closely related species. The slow evolutionary rates inherent to chloroplast (cp) DNA make it difficult to perform lower level taxonomic analyses, particularly at the population level. We characterized the nucleotide variation and investigated the utility of eight noncoding cpDNA regions in four closely related species of the Pilosocereus aurisetus group (Cactaceae), an endemic taxon of eastern South America. The plastid intergenic spacers 5'-trnS-trnG, 3'-trnS-trnG and trnT-trnL were the most variable regions and were the most useful for lower level taxonomic comparisons, especially when used together. We conclude that an adequate combination of regions alongside indels as an additional character improves the usefulness of cpDNA for phylogenetic studies.

  13. Isolation of avian serotype 3 paramyxoviruses from imported caged birds in Israel.

    Science.gov (United States)

    Shihmanter, E; Weisman, Y; Lublin, A; Mahani, S; Panshin, A; Lipkind, M

    1998-01-01

    Ten avian serotype 3 paramyxoviruses were isolated for the first time in Israel from passerine and psittacine imported caged birds. The birds were submitted for investigation of an illness characterized by nonspecific signs of weakness, anorexia, vomiting, and sneezing. In addition, only the parakeets developed specific neurologic signs. In bacteriologic and pathologic investigation, cachexia and diarrhea were observed in both groups of birds. In psittacines, considerable alterations were observed in lungs, liver, and spleen. Some nonviral pathogens were occasionally isolated. The isolates appeared to belong to serotype 3b avian paramyxovirus (APMV), the prototype strain of which is APMV-3b/parakeet/Netherlands/449/75. The isolation of APMV-3 viruses from imported caged birds may represent a way of introduction of these viruses into the country.

  14. Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

    OpenAIRE

    Stefflova, Klara,; Thybert, David; Wilson, Michael D.; Streeter, Ian; Aleksic, Jelena; Karagianni, Panagiota; Brazma, Alvis; Adams, David J.; Talianidis, Iannis; Marioni, John C.; Flicek, Paul; Odom, Duncan T.

    2013-01-01

    Summary To mechanistically characterize the microevolutionary processes active in altering transcription factor (TF) binding among closely related mammals, we compared the genome-wide binding of three tissue-specific TFs that control liver gene expression in six rodents. Despite an overall fast turnover of TF binding locations between species, we identified thousands of TF regions of highly constrained TF binding intensity. Although individual mutations in bound sequence motifs can influence ...

  15. Algal culture studies related to a Closed Ecological Life Support System (CELSS)

    Science.gov (United States)

    Radmer, R.; Behrens, P.; Fernandez, E.; Ollinger, O.; Howell, C.; Venables, A.; Huggins, D.; Gladue, R.

    1984-01-01

    In many respects, algae would be the ideal plant component for a biologically based controlled life support system, since they are eminently suited to the closely coupled functions of atmosphere regeneration and food production. Scenedesmus obliquus and Spirulina platensis were grown in three continuous culture apparatuses. Culture vessels their operation and relative merits are described. Both light and nitrogen utilization efficiency are examined. Long term culture issues are detailed and a discussion of a plasmid search in Spirulina is included.

  16. Identification of a cysteine protease closely related to interleukin-1 beta-converting enzyme.

    Science.gov (United States)

    Faucheu, C; Blanchet, A M; Collard-Dutilleul, V; Lalanne, J L; Diu-Hercend, A

    1996-02-15

    The present study describes the identification and molecular cloning of a new member of the interleukin-1 beta-converting enzyme (ICE) family denoted transcript Y (TY). TY is very closely related to both ICE (51% amino acid identity) and a protein named transcript X (TX) (75% amino acid identity) that we recently identified [Faucheu, C., Diu, A., Chan, A.W.E., Blanchet, A.-M., Miossec, C., Hervé, F.,Collard-Dutilleul, V., Gu, Y., Aldape, R., Lippke, J., Rocher, C., Su, M.S.-S., Livingston, D.J., Hercend, T. & Lalanne, J.-L. (1995) EMBO J. 14, 1914-1922]. The amino acids that are implicated in both the ICE catalytic site and in the PI aspartate-binding pocket are conserved in TY. Within the ICE gene family, TY belongs to a subfamily of proteins closely related to the prototype ICE protein. Using transfection experiments into mammalian cells, we demonstrate that TY has protease activity on its own precursor and that this activity is dependent on the presence of a cysteine residue at position 245. However, despite the close similarity between TY and ICE active sites, TY fails to process the interleukin-1 beta precursor. In addition, as already observed for ICE and TX, TY is able to induce apoptosis when overexpressed in COS cells. TY therefore represents a new member of the growing family of apoptosis-inducing ICE-related cysteine proteases.

  17. Perspectives of patients, close relatives, nurses, and physicians on end-of-life medication management.

    Science.gov (United States)

    Dees, Marianne K; Geijteman, Eric C T; Dekkers, Wim J M; Huisman, Bregje A A; Perez, Roberto S G M; van Zuylen, Lia; van der Heide, Agnes; van Leeuwen, Evert

    2017-08-14

    Our aim was to gain insight into the perspectives of patients, close relatives, nurses, and physicians on medication management for patients with a life expectancy of less than 3 months. We conducted an empirical multicenter study with a qualitative approach, including in-depth interviews with patients, relatives, nurses, specialists, and general practitioners (GPs). We used the constant comparative method and ATLAS.ti (v. 7.1) software for our analysis. Saturation occurred after 18 patient cases (76 interviews). Some 5 themes covering 18 categories were identified: (1) priorities in end-of-life care, such as symptom management and maintaining hope; (2) appropriate medication use, with attention to unnecessary medication and deprescription barriers; (3) roles in decision making, including physicians in the lead, relatives' advocacy, and pharmacists as suppliers; (4) organization and communication (e.g., transparency of tasks and end-of-life conversations); and (5) prerequisites about professional competence, accessibility and quality of medical records, and financial awareness. Patients, relatives, nurses, specialists, and GPs varied in their opinions about these themes. This study adds to our in-depth understanding of the complex practice of end-of-life medication management. It provides knowledge about the diversity of the perspectives of patients, close relatives, nurses, and physicians regarding beliefs, attitudes, knowledge, skills, behavior, work setting, the health system, and cultural factors related to the matter. Our results might help to draw an interdisciplinary end-of-life medication management guide aimed at stimulating a multidisciplinary and patient-centered pharmacotherapeutic care approach.

  18. Oviposition preferences for ethanol depend on spatial arrangement and differ dramatically among closely related Drosophila species.

    Science.gov (United States)

    Sumethasorn, Matt; Turner, Thomas L

    2016-11-15

    Recent work on the model fly Drosophila melanogaster has reported inconsistencies in their preference for laying eggs on intermediate concentrations of ethanol. In this study, we resolve this discrepancy by showing that this species strongly prefers ovipositing on ethanol when it is close to a non-ethanol substrate, but strongly avoids ethanol when options are farther apart. We also show fluidity of these behaviors among other Drosophila species: D. melanogaster is more responsive to ethanol than close relatives in that it prefers ethanol more than other species in the close-proximity case, but avoids ethanol more than other species in the distant case. In the close-proximity scenario, the more ethanol-tolerant species generally prefer ethanol more, with the exception of the island endemic D. santomea This species has the lowest tolerance in the clade, but behaves like D. melanogaster We speculate that this could be an adaptation to protect eggs from parasites or predators such as parasitoid wasps, as larvae migrate to non-toxic substrates after hatching. These natural differences among species are an excellent opportunity to study how genes and brains evolve to alter ethanol preferences, and provide an interesting model for genetic variation in preferences in other organisms, including humans.

  19. Evidence for Retrovirus and Paramyxovirus Infection of Multiple Bat Species in China

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    Lihong Yuan

    2014-05-01

    Full Text Available Bats are recognized reservoirs for many emerging zoonotic viruses of public health importance. Identifying and cataloguing the viruses of bats is a logical approach to evaluate the range of potential zoonoses of bat origin. We characterized the fecal pathogen microbiome of both insectivorous and frugivorous bats, incorporating 281 individual bats comprising 20 common species, which were sampled in three locations of Yunnan province, by combining reverse transcription polymerase chain reaction (RT-PCR assays and next-generation sequencing. Seven individual bats were paramyxovirus-positive by RT-PCR using degenerate primers, and these paramyxoviruses were mainly classified into three genera (Rubulavirus, Henipavirus and Jeilongvirus. Various additional novel pathogens were detected in the paramyxovirus-positive bats using Illumina sequencing. A total of 7066 assembled contigs (≥200 bp were constructed, and 105 contigs matched eukaryotic viruses (of them 103 belong to 2 vertebrate virus families, 1 insect virus, and 1 mycovirus, 17 were parasites, and 4913 were homologous to prokaryotic microorganisms. Among the 103 vertebrate viral contigs, 79 displayed low identity (<70% to known viruses including human viruses at the amino acid level, suggesting that these belong to novel and genetically divergent viruses. Overall, the most frequently identified viruses, particularly in bats from the family Hipposideridae, were retroviruses. The present study expands our understanding of the bat virome in species commonly found in Yunnan, China, and provides insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into humans.

  20. Sequence motifs and prokaryotic expression of the reptilian paramyxovirus fusion protein

    Science.gov (United States)

    Franke, J.; Batts, W.N.; Ahne, W.; Kurath, G.; Winton, J.R.

    2006-01-01

    Fourteen reptilian paramyxovirus isolates were chosen to represent the known extent of genetic diversity among this novel group of viruses. Selected regions of the fusion (F) gene were sequenced, analyzed and compared. The F gene of all isolates contained conserved motifs homologous to those described for other members of the family Paramyxoviridae including: signal peptide, transmembrane domain, furin cleavage site, fusion peptide, N-linked glycosylation sites, and two heptad repeats, the second of which (HRB-LZ) had the characteristics of a leucine zipper. Selected regions of the fusion gene of isolate Gono-GER85 were inserted into a prokaryotic expression system to generate three recombinant protein fragments of various sizes. The longest recombinant protein was cleaved by furin into two fragments of predicted length. Western blot analysis with virus-neutralizing rabbit-antiserum against this isolate demonstrated that only the longest construct reacted with the antiserum. This construct was unique in containing 30 additional C-terminal amino acids that included most of the HRB-LZ. These results indicate that the F genes of reptilian paramyxoviruses contain highly conserved motifs typical of other members of the family and suggest that the HRB-LZ domain of the reptilian paramyxovirus F protein contains a linear antigenic epitope. ?? Springer-Verlag 2005.

  1. Relational mobility explains between- and within-culture differences in self-disclosure to close friends.

    Science.gov (United States)

    Schug, Joanna; Yuki, Masaki; Maddux, William

    2010-10-01

    In the current research, we tested a novel explanation for previously demonstrated findings that East Asians disclose less personal information to other people than do Westerners. We propose that both between- and within-culture differences in self-disclosure to close friends may be explained by the construct of relational mobility, the general degree to which individuals in a society have opportunities to form new relationships and terminate old ones. In Study 1, we found that cross-cultural differences (Japan vs. United States) in self-disclosure to a close friend were mediated by individuals' perceptions of relational mobility. In Study 2, two separate measures of relational mobility predicted self-disclosure within a single culture (Japan), and this relationship was mediated by the motivation to engage in self-disclosure to strengthen personal relationships. We conclude that societies and social contexts higher in relational mobility (in which relationships can be formed and dissolved relatively easily) produce stronger incentives for self-disclosure as a social-commitment device.

  2. Power, attraction, and reference in macrolevel social relations: An analysis of closed groups and closed societies based on the psychology of the “Soviet person”

    Directory of Open Access Journals (Sweden)

    Radina Nadezhda K.

    2017-03-01

    Full Text Available In this article the features of social-relationship systems are analyzed based on the data from a sociopsychological empirical study conducted in two stages (2002 and 2014 on a large sample with the help of g. Kelly’s Repertory grid Technique. A. V. Petrovsky’s three-factor interpersonal-relationships model as interpreted for closed groups by M. Yu. Kondratev and the concept of the closed society as described by Karl Popper provide the foundation for the theoretical hypothesis we tested. The empirical data obtained in 2002 came from 391 participants of different ages who were living in provincial towns in the Nizhny Novgorod region. The elderly respondents (232 people had lived almost all their lives under the Soviet regime; the middle-aged respondents (159 people got their education and started their careers in the USSR. Soviet society is considered to be closed because of its authoritarian and collectivist nature, static social structure, and dogmatic ideology. It is argued that both closed societies and closed groups are characterized by a rigid hierarchical social structure, isolation from other systems, and depersonalization of social relations. We have proved that members of a closed group and citizens of a closed society have similar social-relationship matrices.

  3. SELECTION OF PHYLOGENETICALLY CLOSELY-RELATED YERSINIA PESTIS STRAINS DIFFERING IN THEIR VIRULENCE FOR GUINEA PIGS

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    N. V. Anisimov

    2015-01-01

    Full Text Available Genomic, transcriptome or (and proteomic comparison of closely related virulent and avirulent microbial strains underlies the search for new pathogenicity factors, potential molecular targets for etiotropic therapy, vaccine prevention and immunotherapy of infectious diseases. This investigation was aimed in testing the ability of method of testicular animalization to select phylogenetically close pairs of Y. pestis strains, which dramatically differ in their pathogenicity for guinea pigs, from the populations of as a rule subcutaneously avirulent for guinea pigs “vole” strains of the plague pathogen. Animalization of Y. pestis cultures were performed on guinea pig males by fourfold testicular passage with reducing infective dose. There was no correlation between the ability to cause generalized infectious process (death after testicular and subcutaneous infection of guinea pigs, but testicular passages made it possible to enrich bacterial culture with a portion of microbes displaying high virulence after subcutaneous infection of this animal species. The methodical approach under study can be successfully applied for selection of pairs of phylogenetically closely related bacterial strains, dramatically differing in their degrees of selective virulence. 

  4. Origins and close relatives of a semi-domesticated neotropical fruit tree: Chrysophyllum cainito (Sapotaceae).

    Science.gov (United States)

    Petersen, Jennifer J; Parker, Ingrid M; Potter, Daniel

    2012-03-01

    Understanding patterns and processes associated with domestication has implications for crop development and agricultural biodiversity conservation. Semi-domesticated crops provide excellent opportunities to examine the interplay of natural and anthropogenic influences on plant evolution. The domestication process has not been thoroughly examined in many tropical perennial crop species. Chrysophyllum cainito (Sapotaceae), the star apple or caimito, is a semi-domesticated species widely cultivated for its edible fruits. It is known to be native to the neotropics, but the precise geographic origins of wild and cultivated forms are unresolved. We used nuclear ribosomal ITS sequences to infer phylogenetic relationships among C. cainito and close relatives (section Chrysophyllum). We employed phylogeographic approaches using ITS and plastid sequence data to determine geographic origins and center(s) of domestication of caimito. ITS data suggest a close relationship between C. cainito and C. argenteum. Plastid haplotype networks reveal several haplotypes unique to individual taxa but fail to resolve distinct lineages for either C. cainito or C. argenteum. Caimito populations from northern Mesoamerica and the Antilles exhibit a subset of the genetic diversity found in southern Mesoamerica. In Panama, cultivated caimito retains high levels of the diversity seen in wild populations. Chrysophyllum cainito is most closely related to a clade containing Central and South American C. argenteum, including subsp. panamense. We hypothesize that caimito is native to southern Mesoamerica and was domesticated from multiple wild populations in Panama. Subsequent migration into northern Mesoamerica and the Antilles was mediated by human cultivation.

  5. Genome Annotation Transfer Utility (GATU: rapid annotation of viral genomes using a closely related reference genome

    Directory of Open Access Journals (Sweden)

    Upton Chris

    2006-06-01

    Full Text Available Abstract Background Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics – Canada http://www.virology.ca, we found that researchers were unnecessarily spending time annotating viral genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU, to transfer annotations from a previously annotated reference genome to a new target genome, thereby greatly reducing this laborious task. Results GATU transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. Conclusion GATU greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring reference genome

  6. Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome.

    Science.gov (United States)

    Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris

    2006-06-13

    Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics - Canada http://www.virology.ca, we found that researchers were unnecessarily spending time annotating viral genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated reference genome to a new target genome, thereby greatly reducing this laborious task. GATU transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. GATU greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring reference genome annotations to the target genome. The program is freely

  7. New criteria for selecting the origin of DNA replication in Wolbachia and closely related bacteria

    Directory of Open Access Journals (Sweden)

    Baldo Laura

    2007-06-01

    Full Text Available Abstract Background The annotated genomes of two closely related strains of the intracellular bacterium Wolbachia pipientis have been reported without the identifications of the putative origin of replication (ori. Identifying the ori of these bacteria and related alpha-Proteobacteria as well as their patterns of sequence evolution will aid studies of cell replication and cell density, as well as the potential genetic manipulation of these widespread intracellular bacteria. Results Using features that have been previously experimentally verified in the alpha-Proteobacterium Caulobacter crescentus, the origin of DNA replication (ori regions were identified in silico for Wolbachia strains and eleven other related bacteria belonging to Ehrlichia, Anaplasma, and Rickettsia genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in C. crescentus. The Wolbachia ori boundary genes were found to be hemE and COG1253 protein (CBS domain protein. Comparisons of the putative ori region among related Wolbachia strains showed higher conservation of bases within binding sites. Conclusion The sequences of the ori regions described here are only similar among closely related bacteria while fundamental characteristics like presence of DnaA and IHF binding sites as well as the boundary genes are more widely conserved. The relative paucity of CtrA binding sites in the ori regions, as well as the absence of key enzymes associated with DNA replication in the respective genomes, suggest that several of these obligate intracellular bacteria may have altered replication mechanisms. Based on these analyses, criteria are set forth for identifying the ori region in genome sequencing projects.

  8. Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi.

    Science.gov (United States)

    Torruella, Guifré; de Mendoza, Alex; Grau-Bové, Xavier; Antó, Meritxell; Chaplin, Mark A; del Campo, Javier; Eme, Laura; Pérez-Cordón, Gregorio; Whipps, Christopher M; Nichols, Krista M; Paley, Richard; Roger, Andrew J; Sitjà-Bobadilla, Ariadna; Donachie, Stuart; Ruiz-Trillo, Iñaki

    2015-09-21

    The Opisthokonta are a eukaryotic supergroup divided in two main lineages: animals and related protistan taxa, and fungi and their allies [1, 2]. There is a great diversity of lifestyles and morphologies among unicellular opisthokonts, from free-living phagotrophic flagellated bacterivores and filopodiated amoebas to cell-walled osmotrophic parasites and saprotrophs. However, these characteristics do not group into monophyletic assemblages, suggesting rampant convergent evolution within Opisthokonta. To test this hypothesis, we assembled a new phylogenomic dataset via sequencing 12 new strains of protists. Phylogenetic relationships among opisthokonts revealed independent origins of filopodiated amoebas in two lineages, one related to fungi and the other to animals. Moreover, we observed that specialized osmotrophic lifestyles evolved independently in fungi and protistan relatives of animals, indicating convergent evolution. We therefore analyzed the evolution of two key fungal characters in Opisthokonta, the flagellum and chitin synthases. Comparative analyses of the flagellar toolkit showed a previously unnoticed flagellar apparatus in two close relatives of animals, the filasterean Ministeria vibrans and Corallochytrium limacisporum. This implies that at least four different opisthokont lineages secondarily underwent flagellar simplification. Analysis of the evolutionary history of chitin synthases revealed significant expansions in both animals and fungi, and also in the Ichthyosporea and C. limacisporum, a group of cell-walled animal relatives. This indicates that the last opisthokont common ancestor had a complex toolkit of chitin synthases that was differentially retained in extant lineages. Thus, our data provide evidence for convergent evolution of specialized lifestyles in close relatives of animals and fungi from a generalist ancestor. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

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    Susan R. Strickler

    2015-02-01

    Full Text Available Background. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using the coding sequence from Solanum lycopersicum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and the genomic sequence from S. lycopersicum ‘Heinz’, an heirloom line, S. lycopersicum ‘Yellow Pear’, and two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato.Results. Divergence date estimates suggest that the divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 25 genes in our analysis had sites with evidence of positive selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these genotypes, likely as a result of introgression and incomplete lineage sorting, a primary phylogenetic history was strongly supported.Conclusions. Based on analysis of these genotypes, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication or selection occurring post-domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an

  10. Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

    Science.gov (United States)

    Bombarely, Aureliano; Munkvold, Jesse D.; York, Thomas; Menda, Naama; Martin, Gregory B.; Mueller, Lukas A.

    2015-01-01

    Background. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using the coding sequence from Solanum lycopersicum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and the genomic sequence from S. lycopersicum ‘Heinz’, an heirloom line, S. lycopersicum ‘Yellow Pear’, and two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato. Results. Divergence date estimates suggest that the divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 25 genes in our analysis had sites with evidence of positive selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these genotypes, likely as a result of introgression and incomplete lineage sorting, a primary phylogenetic history was strongly supported. Conclusions. Based on analysis of these genotypes, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication or selection occurring post-domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful

  11. Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives.

    Science.gov (United States)

    Strickler, Susan R; Bombarely, Aureliano; Munkvold, Jesse D; York, Thomas; Menda, Naama; Martin, Gregory B; Mueller, Lukas A

    2015-01-01

    Background. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using the coding sequence from Solanum lycopersicum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and the genomic sequence from S. lycopersicum 'Heinz', an heirloom line, S. lycopersicum 'Yellow Pear', and two of cultivated tomato's closest relatives, S. galapagense and S. pimpinellifolium, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato. Results. Divergence date estimates suggest that the divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 25 genes in our analysis had sites with evidence of positive selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these genotypes, likely as a result of introgression and incomplete lineage sorting, a primary phylogenetic history was strongly supported. Conclusions. Based on analysis of these genotypes, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication or selection occurring post-domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful in

  12. Two closely related species of Caloplaca (Teloschistaceae, Lichenes from the Namib Desert

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    I. Kärnefelt

    1988-12-01

    Full Text Available The anatomical and reproductive adaptations of two closely related lichen species.  Caloplaca elegantissima (Nyl. Zahlbr. and C. namibensis Karnef., sp. nov., occurring in the outer Namib fog desert, are discussed. Both species belong to the cmstose forms, frequently found in the remarkably rich lichen communities, which largely depend on fog precipitation for their water supply. Both species are endemic to the Namib Desert. They are mainly distributed in South West Africa/Namibia but also extend into south-western Angola. The asexual isidiate species.  C. namibensis Karnef., is described as new.

  13. Complete genome sequence of avian paramyxovirus (APMV serotype 5 completes the analysis of nine APMV serotypes and reveals the longest APMV genome.

    Directory of Open Access Journals (Sweden)

    Arthur S Samuel

    Full Text Available BACKGROUND: Avian paramyxoviruses (APMV consist of nine known serotypes. The genomes of representatives of all APMV serotypes except APMV type 5 have recently been fully sequenced. Here, we report the complete genome sequence of the APMV-5 prototype strain budgerigar/Kunitachi/74. METHODOLOGY/PRINCIPAL FINDINGS: APMV-5 Kunitachi virus is unusual in that it lacks a virion hemagglutinin and does not grow in the allantoic cavity of embryonated chicken eggs. However, the virus grew in the amniotic cavity of embryonated chicken eggs and in twelve different established cell lines and two primary cell cultures. The genome is 17,262 nucleotides (nt long, which is the longest among members of genus Avulavirus, and encodes six non-overlapping genes in the order of 3'N-P/V/W-M-F-HN-L-5' with intergenic regions of 4-57 nt. The genome length follows the 'rule of six' and contains a 55-nt leader sequence at the 3'end and a 552 nt trailer sequence at the 5' end. The phosphoprotein (P gene contains a conserved RNA editing site and is predicted to encode P, V, and W proteins. The cleavage site of the F protein (G-K-R-K-K-R downward arrowF conforms to the cleavage site motif of the ubiquitous cellular protease furin. Consistent with this, exogenous protease was not required for virus replication in vitro. However, the intracerebral pathogenicity index of APMV-5 strain Kunitachi in one-day-old chicks was found to be zero, indicating that the virus is avirulent for chickens despite the presence of a polybasic F cleavage site. CONCLUSIONS/SIGNIFICANCE: Phylogenetic analysis of the sequences of the APVM-5 genome and proteins versus those of the other APMV serotypes showed that APMV-5 is more closely related to APMV-6 than to the other APMVs. Furthermore, these comparisons provided evidence of extensive genome-wide divergence that supports the classification of the APMVs into nine separate serotypes. The structure of the F cleavage site does not appear to be a

  14. Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives.

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    Jaime E Blair

    Full Text Available To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based "supergene" approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred.

  15. Species Tree Estimation for the Late Blight Pathogen, Phytophthora infestans, and Close Relatives

    Science.gov (United States)

    Blair, Jaime E.; Coffey, Michael D.; Martin, Frank N.

    2012-01-01

    To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based “supergene” approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred. PMID:22615869

  16. Comparative genome analysis of the closely related Synechocystis strains PCC 6714 and PCC 6803.

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    Kopf, Matthias; Klähn, Stephan; Pade, Nadin; Weingärtner, Christian; Hagemann, Martin; Voß, Björn; Hess, Wolfgang R

    2014-06-01

    Synechocystis sp. PCC 6803 is the most popular cyanobacterial model for prokaryotic photosynthesis and for metabolic engineering to produce biofuels. Genomic and transcriptomic comparisons between closely related bacteria are powerful approaches to infer insights into their metabolic potentials and regulatory networks. To enable a comparative approach, we generated the draft genome sequence of Synechocystis sp. PCC 6714, a closely related strain of 6803 (16S rDNA identity 99.4%) that also is amenable to genetic manipulation. Both strains share 2838 protein-coding genes, leaving 845 unique genes in Synechocystis sp. PCC 6803 and 895 genes in Synechocystis sp. PCC 6714. The genetic differences include a prophage in the genome of strain 6714, a different composition of the pool of transposable elements, and a ∼ 40 kb genomic island encoding several glycosyltransferases and transport proteins. We verified several physiological differences that were predicted on the basis of the respective genome sequence. Strain 6714 exhibited a lower tolerance to Zn(2+) ions, associated with the lack of a corresponding export system and a lowered potential of salt acclimation due to the absence of a transport system for the re-uptake of the compatible solute glucosylglycerol. These new data will support the detailed comparative analyses of this important cyanobacterial group than has been possible thus far. Genome information for Synechocystis sp. PCC 6714 has been deposited in Genbank (accession no AMZV01000000). © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  17. Genetic basis of hybrid male sterility among three closely related species of Drosophila.

    Science.gov (United States)

    Mishra, Paras Kumar; Singh, B N

    2005-05-01

    The genetic basis of hybrid male sterility among three closely related species, Drosophila bipectinata, D. parabipectinata and D. malerkotliana has been investigated by using backcross analysis methods. The role of Y chromosome, major hybrid sterility (MHS) genes (genetic factors) and cytoplasm (non-genetic factor) have been studied in the hybrids of these three species. In the species pair, bipectinata--parabipectinata, Y chromosome introgression of parabipectinata in the genomic background of bipectinata and the reciprocal Y chromosome introgression were unsuccessful as all males in second backcross generation were sterile. Neither MHS genes nor cytoplasm was found important for sterility. This suggests the involvement of X-Y, X-autosomes or polygenic interactions in hybrid male sterility. In bipectinata--malerkotliana and parabipectinata--malerkotliana species pairs, Y chromosome substitution in reciprocal crosses did not affect male fertility. Backcross analyses also show no involvement of MHS genes or cytoplasm in hybrid male sterility in these two species pairs. Therefore, X- autosome interaction or polygenic interaction is supposed to be involved in hybrid male sterility in these two species pairs. These findings also provide evidence that even in closely related species, genetic interactions underlying hybrid male sterility may vary.

  18. Close relation between quantum interference in molecular conductance and diradical existence.

    Science.gov (United States)

    Tsuji, Yuta; Hoffmann, Roald; Strange, Mikkel; Solomon, Gemma C

    2016-01-26

    An empirical observation of a relationship between a striking feature of electronic transmission through a π-system, destructive quantum interference (QI), on one hand, and the stability of diradicals on the other, leads to the proof of a general theorem that relates the two. Subject to a number of simplifying assumptions, in a π-electron system, QI occurs when electrodes are attached to those positions of an N-carbon atom N-electron closed-shell hydrocarbon where the matrix elements of the Green's function vanish. These zeros come in two types, which are called easy and hard. Suppose an N+2 atom, N+2 electron hydrocarbon is formed by substituting 2 CH2 groups at two atoms, where the electrodes were. Then, if a QI feature is associated with electrode attachment to the two atoms of the original N atom system, the resulting augmented N+2 molecule will be a diradical. If there is no QI feature, i.e., transmission of current is normal if electrodes are attached to the two atoms, the resulting hydrocarbon will not be a diradical but will have a classical closed-shell electronic structure. Moreover, where a diradical exists, the easy zero is associated with a nondisjoint diradical, and the hard zero is associated with a disjoint one. A related theorem is proven for deletion of two sites from a hydrocarbon.

  19. Do plant traits predict the competitive abilities of closely related species?

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    Schwartz, Lauren M; Gibson, David J; Young, Bryan G

    2015-12-31

    Invasive species are a threat to every ecosystem. There is a strong incentive to predict which species will become invasive before they become too widespread and unmanageable. Different approaches have been advocated to assess invasive species potential. These include examining plant functional traits, quantifying competitive ability and phylogenetic comparison. In this study, we conducted experiments based on the above approaches in a multi-year, temporally replicated, set of experiments to compare these assessment methods to determine the invasive potential of Japanese chaff flower (Achyranthes japonica). We compared plant traits and competitive ability of Japanese chaff flower with two agricultural invasive species, Palmer amaranth (Amaranthus palmeri) and tall waterhemp (Amaranthus tuberculatus), and one endangered plant species, bloodleaf (Iresine rhizomatosa), in the Amaranthaceae. Additionally, we assessed the invasive potential based on each of these approaches and determined the degree of agreement between them. A relatively conservative assessment integrating all three approaches would be that the competitive ability of closely related individuals with similar functional traits would share invasive potential. In a greenhouse experiment, each of the study species and soya beans were grown as monocultures and were evaluated to assess the drawdown of an aboveground (light) and a belowground (nitrogen) resource. In a field experiment, each study species was grown at varying densities per 15-cm-diameter pot with or without one or two soya bean plants, to simulate relative densities for soya beans grown in 38- and 76-cm-wide row spacing, respectively. In addition, Japanese chaff flower seedlings were planted either as un-manipulated seedlings or as a seedling cut back to the soil surface at the four-node stage (cut Japanese chaff flower) at which point seedlings have reached a perennial growth stage. The greenhouse experiment showed that each species drew down

  20. Language Adaptation for Extending Post-Editing Estimates for Closely Related Languages

    Directory of Open Access Journals (Sweden)

    Rios Miguel

    2016-10-01

    Full Text Available This paper presents an open-source toolkit for predicting human post-editing efforts for closely related languages. At the moment, training resources for the Quality Estimation task are available for very few language directions and domains. Available resources can be expanded on the assumption that MT errors and the amount of post-editing required to correct them are comparable across related languages, even if the feature frequencies differ. In this paper we report a toolkit for achieving language adaptation, which is based on learning new feature representation using transfer learning methods. In particular, we report performance of a method based on Self-Taught Learning which adapts the English-Spanish pair to produce Quality Estimation models for translation from English into Portuguese, Italian and other Romance languages using the publicly available Autodesk dataset.

  1. Solubilization of matrix protein M1/M from virions occurs at different pH for orthomyxo- and paramyxoviruses.

    Science.gov (United States)

    Zhirnov, O P

    1990-05-01

    Enveloped viruses, of which the orthomyxo- and paramyxoviruses are members, are known to be uncoated by nonionic detergents in a salt concentration-dependent manner. In this study we have shown that detergent uncoating of myxoviruses depends not only on salt concentration but also on pH. Treatment of orthomyxoviruses with Nonidet-P40 or Triton N-101 at low salt concentrations results in solubilization of surface virion glycopolypeptides in alkaline and neutral pH (9.0-6.5), but in acidic pH (6.0-5.0) the viral matrix protein M1 is also removed, and the viral ribonucleoprotein complex is released. Conversely, the paramyxovirus matrix protein M is more completely solubilized in alkaline pH (pH 9.0) than in neutral and acidic pH 7.4-5.0. The described pH-dependent differences are discussed in terms of orthomyxo- and paramyxovirus uncoating in target cells.

  2. Closely related Campylobacter jejuni strains from different sources reveal a generalist rather than a specialist lifestyle

    Science.gov (United States)

    2011-01-01

    Background Campylobacter jejuni and Campylobacter coli are human intestinal pathogens of global importance. Zoonotic transmission from livestock animals or animal-derived food is the likely cause for most of these infections. However, little is known about their general and host-specific mechanisms of colonization, or virulence and pathogenicity factors. In certain hosts, Campylobacter species colonize persistently and do not cause disease, while they cause acute intestinal disease in humans. Results Here, we investigate putative host-specificity using phenotypic characterization and genome-wide analysis of genetically closely related C. jejuni strains from different sources. A collection of 473 fresh Campylobacter isolates from Germany was assembled between 2006 and 2010 and characterized using MLST. A subset of closely related C. jejuni strains of the highly prevalent sequence type ST-21 was selected from different hosts and isolation sources. PCR typing of strain-variable genes provided evidence that some genes differed between these strains. Furthermore, phenotypic variation of these strains was tested using the following criteria: metabolic variation, protein expression patterns, and eukaryotic cell interaction. The results demonstrated remarkable phenotypic diversity within the ST-21 group, which however did not correlate with isolation source. Whole genome sequencing was performed for five ST-21 strains from chicken, human, bovine, and food sources, in order to gain insight into ST-21 genome diversity. The comparisons showed extensive genomic diversity, primarily due to recombination and gain of phage-related genes. By contrast, no genomic features associated with isolation source or host were identified. Conclusions The genome information and phenotypic data obtained in vitro and in a chicken infection model provided little evidence of fixed adaptation to a specific host. Instead, the dominant C. jejuni ST-21 appeared to be characterized by phenotypic

  3. Identification of a fungi-specific lineage of protein kinases closely related to tyrosine kinases.

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    Zhongtao Zhao

    Full Text Available Tyrosine kinases (TKs specifically catalyze the phosphorylation of tyrosine residues in proteins and play essential roles in many cellular processes. Although TKs mainly exist in animals, recent studies revealed that some organisms outside the Opisthokont clade also contain TKs. The fungi, as the sister group to animals, are thought to lack TKs. To better understand the origin and evolution of TKs, it is important to investigate if fungi have TK or TK-related genes. We therefore systematically identified possible TKs across the fungal kingdom by using the profile hidden Markov Models searches and phylogenetic analyses. Our results confirmed that fungi lack the orthologs of animal TKs. We identified a fungi-specific lineage of protein kinases (FslK that appears to be a sister group closely related to TKs. Sequence analysis revealed that members of the FslK clade contain all the conserved protein kinase sub-domains and thus are likely enzymatically active. However, they lack key amino acid residues that determine TK-specific activities, indicating that they are not true TKs. Phylogenetic analysis indicated that the last common ancestor of fungi may have possessed numerous members of FslK. The ancestral FslK genes were lost in Ascomycota and Ustilaginomycotina and Pucciniomycotina of Basidiomycota during evolution. Most of these ancestral genes, however, were retained and expanded in Agaricomycetes. The discovery of the fungi-specific lineage of protein kinases closely related to TKs helps shed light on the origin and evolution of TKs and also has potential implications for the importance of these kinases in mushroom fungi.

  4. Identification of a fungi-specific lineage of protein kinases closely related to tyrosine kinases.

    Science.gov (United States)

    Zhao, Zhongtao; Jin, Qiaojun; Xu, Jin-Rong; Liu, Huiquan

    2014-01-01

    Tyrosine kinases (TKs) specifically catalyze the phosphorylation of tyrosine residues in proteins and play essential roles in many cellular processes. Although TKs mainly exist in animals, recent studies revealed that some organisms outside the Opisthokont clade also contain TKs. The fungi, as the sister group to animals, are thought to lack TKs. To better understand the origin and evolution of TKs, it is important to investigate if fungi have TK or TK-related genes. We therefore systematically identified possible TKs across the fungal kingdom by using the profile hidden Markov Models searches and phylogenetic analyses. Our results confirmed that fungi lack the orthologs of animal TKs. We identified a fungi-specific lineage of protein kinases (FslK) that appears to be a sister group closely related to TKs. Sequence analysis revealed that members of the FslK clade contain all the conserved protein kinase sub-domains and thus are likely enzymatically active. However, they lack key amino acid residues that determine TK-specific activities, indicating that they are not true TKs. Phylogenetic analysis indicated that the last common ancestor of fungi may have possessed numerous members of FslK. The ancestral FslK genes were lost in Ascomycota and Ustilaginomycotina and Pucciniomycotina of Basidiomycota during evolution. Most of these ancestral genes, however, were retained and expanded in Agaricomycetes. The discovery of the fungi-specific lineage of protein kinases closely related to TKs helps shed light on the origin and evolution of TKs and also has potential implications for the importance of these kinases in mushroom fungi.

  5. The non-pathogenic Henipavirus Cedar paramyxovirus phosphoprotein has a compromised ability to target STAT1 and STAT2.

    Science.gov (United States)

    Lieu, Kim G; Marsh, Glenn A; Wang, Lin-Fa; Netter, Hans J

    2015-12-01

    Immune evasion by the lethal henipaviruses, Hendra (HeV) and Nipah virus, is mediated by its interferon (IFN) antagonist P gene products, phosphoprotein (P), and the related V and W proteins, which can target the signal transducer and activator of transcription 1 (STAT1) and STAT2 proteins to inhibit IFN/STAT signaling. However, it is not clear if the recently identified non-pathogenic Henipavirus, Cedar paramyxovirus (CedPV), is also able to antagonize the STAT proteins. We performed comparative studies between the HeV P gene products (P/V/W) and CedPV-P (CedPV does not encode V or W) and demonstrate that differences exist in their ability to engage the STAT proteins using immunoprecipitation and quantitative confocal microscopic analysis. In contrast to HeV-P gene encoded proteins, the ability of CedPV-P to interact with and relocalize STAT1 or STAT2 is compromised, correlating with a reduced capacity to inhibit the mRNA synthesis of IFN-inducible gene MxA. Furthermore, infection studies with HeV and CedPV demonstrate that HeV is more potent than CedPV in inhibiting the IFN-α-mediated nuclear accumulation of STAT1. These results strongly suggest that the ability of CedPV to counteract the IFN/STAT response is compromised compared to HeV.

  6. A murine herpesvirus closely related to ubiquitous human herpesviruses causes T-cell depletion.

    Science.gov (United States)

    Patel, Swapneel J; Zhao, Guoyan; Penna, Vinay R; Park, Eugene; Lauron, Elvin J; Harvey, Ian B; Beatty, Wandy L; Plougastel-Douglas, Beatrice; Poursine-Laurent, Jennifer; Fremont, Daved H; Wang, David; Yokoyama, Wayne M

    2017-02-08

    Mouse models of human herpesvirus infections The human roseoloviruses HHV6A, HHV6B, and HHV7 comprise the Roseolovirus genus of the human Betaherpesvirinae subfamily. Infections with these viruses have been implicated in many diseases; however, it has been challenging to establish infections with Roseoloviruses as direct drivers of pathology because they are nearly ubiquitous and display species-specific tropism. Furthermore, controlled study of infection has been hampered by the lack of experimental models, and until now, a mouse roseolovirus has not been identified. Herein we describe a virus that causes severe thymic necrosis in neonatal mice, characterized by a loss of CD4(+) T-cells. These phenotypes resemble those caused by the previously described mouse thymic virus (MTV), a putative herpesvirus that has not been molecularly characterized. By Next Generation sequencing of infected tissue homogenates, we assembled a contiguous 174Kb genome sequence encoding 128 unique predicted open reading frames (ORFs), many of which were most closely related to herpesvirus genes. Moreover, the structure of the virus genome and phylogenetic analysis of multiple genes strongly suggested that this virus is a betaherpesvirus more closely related to the roseoloviruses, HHV6A, HHV6B, and HHV7, than another murine betaherpesvirus, mouse cytomegalovirus (MCMV). As such, we have named this virus murine roseolovirus (MRV) because these data strongly suggest that MRV is a mouse homolog of HHV6A/HHV6B/HHV7.Importance: Herein we describe the complete genome sequence of a novel murine herpesvirus. By sequence and phylogenetic analyses, we show that it is a betaherpesvirus most closely related to the roseoloviruses, human herpesvirus 6A, 6B, and 7. These data combined with physiological similarities with human roseoloviruses collectively suggest that this virus is a murine roseolovirus (MRV), the first definitively described rodent roseolovirus, to our knowledge. Many biological and

  7. Separation of human, bovine, and porcine insulins, three very closely related proteins, by micellar electrokinetic chromatography.

    Science.gov (United States)

    Lamalle, Caroline; Roland, Diane; Crommen, Jacques; Servais, Anne-Catherine; Fillet, Marianne

    2015-10-01

    Human, bovine, and porcine insulins are small proteins with very closely related amino acid sequences, which makes their separation challenging. In this study, we took advantage of the high-resolution power of CE, and more particularly of micellar electrokinetic chromatography, to separate those biomolecules. Among several surfactants, perfluorooctanoic acid ammonium salt was selected. Then, using a design of experiments approach, the optimal BGE composition was found to consist of 50 mM ammonium acetate pH 9.0, 65 mM perfluorooctanoic acid ammonium salt, and 4% MeOH. The three insulins could be separated within 12 min with a satisfactory resolution. This method could be useful to detect possible counterfeit pharmaceutical formulations. Indeed, it would be easy to determine if human insulin was replaced by bovine or porcine insulin.

  8. TB-infected deer are more closely related than non-infected deer.

    Science.gov (United States)

    Blanchong, Julie A; Scribner, Kim T; Kravchenko, Alexandra N; Winterstein, Scott R

    2007-02-22

    Identifying mechanisms of pathogen transmission is critical to controlling disease. Social organization should influence contacts among individuals and thus the distribution and spread of disease within a population. Molecular genetic markers can be used to elucidate mechanisms of disease transmission in wildlife populations without undertaking detailed observational studies to determine probable contact rates. Estimates of genealogical relationships within a bovine tuberculosis-infected white-tailed deer (Odocoileus virginianus) population indicated that infected deer were significantly more closely related than non-infected deer suggesting that contact within family groups was a significant mechanism of disease transmission. Results demonstrate that epidemiological models should incorporate aspects of host ecology likely to affect the probability of disease transmission.

  9. [Duties of TB patients or suspected patients and their close relations].

    Science.gov (United States)

    Zielonka, Tadeusz M

    2015-01-01

    The effective laws impose the duty upon TB patients or persons suspected to have TB as well as their close relations to undergo compulsory sanitary and epidemiological examinations. Furthermore, treatment is also mandatory and in case of infective patients hospitalization and isolation. Duty does not however denote enforcement, which is required in certain particularly dangerous infectious diseases. Poland operates a system of mandatory TB vaccination applicable, today, only to infants. Persons suspected of TB have the obligation to provide necessary information helping in diagnosing the disease or helping to find the source of infection and transmission of the disease. TB patients are under obligation to discontinue performing their work to prevent the disease from spreading to other persons.

  10. Cell wall swelling, fracture mode, and the mechanical properties of cherry fruit skins are closely related.

    Science.gov (United States)

    Brüggenwirth, Martin; Knoche, Moritz

    2017-04-01

    Cell wall swelling, fracture mode (along the middle lamellae vs. across cell walls), stiffness, and pressure at fracture of the sweet cherry fruit skin are closely related. Skin cracking is a common phenomenon in many crops bearing fleshy fruit. The objectives were to investigate relationships between the mode of fracture, the extent of cell wall swelling, and the mechanical properties of the fruit skin using sweet cherry (Prunus avium) as a model. Cracking was induced by incubating whole fruit in deionised water or by fracturing exocarp segments (ESs) in biaxial tensile tests. The fracture mode of epidermal cells was investigated by light microscopy. In biaxial tensile tests, the anticlinal cell walls of the ES fractured predominantly across the cell walls (rather than along) and showed no cell wall swelling. In contrast, fruit incubated in water fractured predominantly along the anticlinal epidermal cell walls and the cell walls were swollen. Swelling of cell walls also occurred when ESs were incubated in malic acid, in hypertonic solutions of sucrose, or in water. Compared to the untreated controls, these treatments resulted in more frequent fractures along the cell walls, lower pressures at fracture (p fracture), and lower moduli of elasticity (E, i.e., less stiff). Conversely, compared to the untreated controls, incubating the ES in CaCl2 and in high concentrations of ethanol resulted in thinner cell walls, in less frequent fractures along the cell walls, higher E and p fracture. Our study demonstrates that fracture mode, stiffness, and pressure at fracture are closely related to cell wall swelling. A number of other factors, including cultivar, ripening stage, turgor, CaCl2, and malic acid, exert their effects only indirectly, i.e., by affecting cell wall swelling.

  11. Mycorrhizal associations and reproductive isolation in three closely related Orchis species

    Science.gov (United States)

    Jacquemyn, Hans; Brys, Rein; Cammue, Bruno P. A.; Honnay, Olivier; Lievens, Bart

    2011-01-01

    Background and Aims The maintenance of species boundaries in sympatric populations of closely related species requires some kind of reproductive isolation that limits gene flow among species and/or prevents the production of viable progeny. Because in orchids mycorrhizal fungi are needed for seed germination and subsequent seedling establishment, orchid–mycorrhizal associations may be involved in acting as a post-mating barrier. Methods We investigated the strength of post-mating barriers up to the seed germination stage acting between three closely related Orchis species (Orchis anthropophora, O. militaris and O. purpurea) and studied the role of mycorrhizal fungi in hybridization by burying seed packets of pure and hybrid seeds. After retrieval and assessment of seed germination, the fungi associating with protocorms originating from hybrid and pure seeds were determined and compared with those associating with adult individuals using DNA array technology. Results Whereas pre-zygotic post-mating barriers were rather weak in most crosses, post-zygotic post-mating barriers were stronger, particularly when O. purpurea was crossed with O. anthropophora. Germination trials in the field showed that seed germination percentages of hybrid seeds were in most cases lower than those originating from pure crosses. In all species pair combinations, total post-mating reproductive isolation was asymmetric. Protocorms associated with a smaller range of fungal symbionts than adult plants, but there was considerable overlap in mycorrhizal associations between protocorms and their respective parents. Conclusions Our results suggest that mycorrhizal associations contribute little to reproductive isolation. Pre-mating barriers are probably the main factors determining hybridization rates between the investigated species. PMID:21186239

  12. Asymmetric gene introgression in two closely related Orchis species: evidence from morphometric and genetic analyses

    Directory of Open Access Journals (Sweden)

    Jacquemyn Hans

    2012-09-01

    Full Text Available Abstract Background In food-deceptive orchids of the genera Anacamptis, Neotinea and Orchis floral isolation has been shown to be weak, whereas late-acting reproductive barriers are mostly strong, often restricting hybridization to the F1 generation. Only in a few species hybridization extends beyond the F1 generation, giving rise to hybrid swarms. However, little is known about the abundance of later-generation hybrids and what factors drive their occurrence in hybrid populations. In this study, molecular analyses were combined with detailed morphological measurements in a hybrid population of two closely related Orchis species (Orchis militaris and O. purpurea to investigate the hypothesis that the abundance of later-generation hybrids is driven by changes in floral characters after hybridization that exert selective pressures that in turn affect hybridization. Results Both the molecular and morphological data point to extensive genetic and morphological homogenization and asymmetric introgression. Estimating genomic clines from the multi-locus genotype data and testing for deviation from neutrality revealed that 30 out of 113 (27% AFLP markers significantly deviated from neutral expectations. Plants with large floral displays or plant with flowers that resembled more O. purpurea had higher female fitness than plants with small floral displays or plants with flowers resembling more O. militaris, suggesting that directional selection may have contributed to the observed patterns of introgression. Conclusions These results indicate that in closely related orchid species hybridization and gene introgression may be partly driven by selection for floral traits of one of the parental types. However, because some pure individuals were still present in the studied population, the parental species appeared to be sufficiently isolated to survive the challenge of sympatry.

  13. Phenology, growth, and fecundity as determinants of distribution in closely related nonnative taxa

    Science.gov (United States)

    Marushia, Robin G.; Brooks, Matthew L.; Holt, Jodie S.

    2012-01-01

    Invasive species researchers often ask: Why do some species invade certain habitats while others do not? Ecological theories predict that taxonomically related species may invade similar habitats, but some related species exhibit contrasting invasion patterns. Brassica nigra, Brassica tournefortii, and Hirschfeldia incana are dominant, closely related nonnative species that have overlapping, but dissimilar, distributions. Brassica tournefortii is rapidly spreading in warm deserts of the southwestern United States, whereas B. nigra and H. incana are primarily limited to semiarid and mesic regions. We compared traits of B. tournefortii that might confer invasiveness in deserts with those of related species that have not invaded desert ecosystems. Brassica tournefortii, B. nigra and H. incana were compared in controlled experiments conducted outdoors in a mesic site (Riverside, CA) and a desert site (Blue Diamond, NV), and in greenhouses, over 3 yr. Desert and mesic B. tournefortii populations were also compared to determine whether locally adapted ecotypes contribute to desert invasion. Experimental variables included common garden sites and soil water availability. Response variables included emergence, growth, phenology, and reproduction. There was no evidence for B. tournefortii ecotypes, but B. tournefortii had a more rapid phenology than B. nigra or H. incana. Brassica tournefortii was less affected by site and water availability than B. nigra and H. incana, but was smaller and less fecund regardless of experimental conditions. Rapid phenology allows B. tournefortii to reproduce consistently under variable, stressful conditions such as those found in Southwestern deserts. Although more successful in milder, mesic ecosystems, B. nigra and H. incana may be limited by their ability to reproduce under desert conditions. Rapid phenology and drought response partition invasion patterns of nonnative mustards along a gradient of aridity in the southwestern United States

  14. Migratory New World blackbirds (icterids are more neophobic than closely related resident icterids.

    Directory of Open Access Journals (Sweden)

    Claudia Mettke-Hofmann

    Full Text Available Environments undergo short-term and long-term changes due to natural or human-induced events. Animals differ in their ability to cope with such changes which can be related to their ecology. Changes in the environment often elicit avoidance reactions (neophobia which protect animals from dangerous situations but can also inhibit exploration and familiarization with novel situations and thus, learning about new resources. Studies investigating the relationship between a species' ecology and its neophobia have so far been restricted to comparing only a few species and mainly in captivity. The current study investigated neophobia reactions to experimentally-induced changes in the natural environment of six closely-related blackbird species (Icteridae, including two species represented by two distinct populations. For analyses, neophobic reactions (difference in number of birds feeding and time spent feeding with and without novel objects were related to several measures of ecological plasticity and the migratory strategy (resident or migratory of the population. Phylogenetic relationships were incorporated into the analysis. The degree of neophobia was related to migratory strategy with migrants expressing much higher neophobia (fewer birds feeding and for a shorter time with objects present than residents. Furthermore, neophobia showed a relationship to diet breadth with fewer individuals of diet generalists than specialists returning when objects were present supporting the dangerous niche hypothesis. Residents may have evolved lower neophobia as costs of missing out on opportunities may be higher for residents than migrants as the former are restricted to a smaller area. Lower neophobia allows them approaching changes in the environment (e.g. novel objects quickly, thereby securing access to resources. Additionally, residents have a greater familiarity with similar situations in the area than migrants and the latter may, therefore, initially

  15. Differential regulation of two closely related integrative and conjugative elements from Streptococcus thermophilus

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    Carraro Nicolas

    2011-10-01

    Full Text Available Abstract Background Two closely related ICEs, ICESt1 and ICESt3, have been identified in the lactic acid bacterium Streptococcus thermophilus. While their conjugation and recombination modules are almost identical (95% nucleotide identity and their regulation modules related, previous work has demonstrated that transconjugants carrying ICESt3 were generated at rate exceeding by a 1000 factor that of ICESt1. Results The functional regulation of ICESt1 and ICESt3 transcription, excision and replication were investigated under different conditions (exponential growth or stationary phase, DNA damage by exposition to mitomycin C. Analysis revealed an identical transcriptional organization of their recombination and conjugation modules (long unique transcript whereas the transcriptional organization of their regulation modules were found to be different (two operons in ICESt1 but only one in ICESt3 and to depend on the conditions (promoter specific of stationary phase in ICESt3. For both elements, stationary phase and DNA damage lead to the rise of transcript levels of the conjugation-recombination and regulation modules. Whatever the growth culture conditions, excision of ICESt1 was found to be lower than that of ICESt3, which is consistent with weaker transfer frequencies. Furthermore, for both elements, excision increases in stationary phase (8.9-fold for ICESt1 and 1.31-fold for ICESt3 and is strongly enhanced by DNA damage (38-fold for ICESt1 and 18-fold for ICESt3. Although ICEs are generally not described as replicative elements, the copy number of ICESt3 exhibited a sharp increase (9.6-fold after mitomycin C exposure of its harboring strain CNRZ385. This result was not observed when ICESt3 was introduced in a strain deriving ICESt1 host strain CNRZ368, deleted for this element. This finding suggests an impact of the host cell on ICE behavior. Conclusions All together, these results suggest a novel mechanism of regulation shared by ICESt1

  16. The Relation of the Morse Index of Closed Geodesics with the Maslov-type Index of Symplectic Paths

    Institute of Scientific and Technical Information of China (English)

    Chun Gen LIU

    2005-01-01

    In this paper, we consider the relation of the Morse index of a closed geodesic with the Maslov-type index of a path in a symplectic group. More precisely, for a closed geodesic c on a Riemannian manifold M with its linear Poincare map P (a symplectic matrix), we construct a symplectic path γ(t) starting from identity I and ending at P, such that the Morse index of the closed geodesic c equals the Maslov-type index of γ. As an application of this result, we study the parity of the Morse index of any closed geodesic.

  17. Comparative genomics of Japanese Erwinia pyrifoliae strain Ejp617 with closely related erwinias.

    Science.gov (United States)

    Thapa, Shree P; Park, Duck H; Kim, Won S; Choi, Beom S; Lim, Jong S; Choi, Ik Y; Hur, Jang H; Lim, Chun K

    2013-02-01

    Japanese Erwinia pyrifoliae strains cause bacterial shoot blight of pear (BSBP) in Japan. The genetics of Japanese Erwinia remains largely unknown relative to the abundant genomic information available for other Erwinia strains. We compared the genome of Japanese and Korean E. pyrifoliae strains along with those of E. amylovora and E. tasmaniensis. Comparisons with the Korean E. pyrifoliae strain revealed numerous gene insertions/deletions, rearrangements, and inversions in the central regions of the chromosomes. Approximately 80% (2843) of coding DNA sequences (CDSs) are shared by these two genomes which represent about three-quarters of the genome, and there are about 20% unique CDSs. Comparative analysis with closely related erwinias showed that 1942 (more than 50%) core open reading frames (ORF) are shared by all these strains. In addition to two type III secretion systems (hrp/dsp and inv/spa), the genome of Ejp617 encodes numerous virulence factors, including a type VI secretion system, an exopolysaccharide synthesis cluster, and another protein secretion system present in plant pathogenic Erwinia strains. The availability of whole genome sequence should provide a resource to further improve the understanding of pathogenesis in Japanese E. pyrifoliae Ejp617 and to facilitate evolutionary studies among the species of the genus Erwinia.

  18. Genetic Comparison of B. Anthracis and its Close Relatives Using AFLP and PCR Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, P.J.; Hill, K.K.; Laker, M.T.; Ticknor, L.O.; Keim, P.S.

    1999-02-01

    Amplified Fragment length Polymorphism (AFLP) analysis allows a rapid, relatively simple analysis of a large portion of a microbial genome, providing information about the species and its phylogenetic relationship to other microbes (Vos, et al., 1995). The method simply surveys the genome for length and sequence polymorphisms. The pattern identified can be used for comparison to the genomes of other species. Unlike other methods, it does not rely on analysis of a single genetic locus that may bias the interpretation of results and it does not require any prior knowledge of the targeted organism. Moreover, a standard set of reagents can be applied to any species without using species-specific information or molecular probes. The authors are using AFLP's to rapidly identify different bacterial species. A comparison of AFLP profiles generated from a large battery of B. anthracis strains shows very little variability among different isolates (Keim, et al., 1997). By contrast, there is a significant difference between AFLP profiles generated for any B. anthracis strain and even the most closely related Bacillus species. Sufficient variability is apparent among all known microbial species to allow phylogenetic analysis based on large numbers of genetically unlinked loci. These striking differences among AFLP profiles allow unambiguous identification of previously identified species and phylogenetic placement of newly characterized isolates relative to known species based on a large number of independent genetic loci. Data generated thus far show that the method provides phylogenetic analyses that are consistent with other widely accepted phylogenetic methods. However, AFLP analysis provides a more detailed analysis of the targets and samples a much larger portion of the genome. Consequently, it provides an inexpensive, rapid means of characterizing microbial isolates to further differentiate among strains and closely related microbial species. Such information

  19. Genetic variability in apomictic mangosteen (Garcinia mangostana and its close relatives (Garcinia spp. based on ISSR markers

    Directory of Open Access Journals (Sweden)

    SOBIR

    2011-04-01

    Full Text Available Sobir, Poerwanto R, Santosa E, Sinaga S, Mansyah E (2011 Genetic variability in apomictic mangosteen (Garcinia mangostana and its close relatives (Garcinia spp. based on ISSR markers. Biodiversitas 12: 59-63. In order to reveal phylogenetic relationship of mangosteen and several close relatives (Garcinia spp., we employed seven ISSR dinucleotide primer systems on eleven close relatives of mangosteen and 28 mangosteen accessions from four islands in Indonesia (Sumatra, Java, Kalimantan and Lombok. ISSR analysis successfully amplified 43 bands on average 6.1 fragments for each primer system, and these all fragments were polymorphic. Seven close relatives of mangosteen were separated with mangosteen accessions at 0.22 level of dissimilarity, while other four including G. malaccensis, were clustered with mangosteen accessions, this results supported proposal that G. malaccensis was allopolyploid derivative of mangosteen. Clustering pattern among mangosteen accessions, however, not represented their origin, indicated that distribution of the accessions was not linked to their genetic properties.

  20. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable rates of evolution within a core genome

    Science.gov (United States)

    Background: Biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context. We sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricu...

  1. Contrasting Genomic Diversity in Two Closely Related Postharvest Pathogens: Penicillium digitatum and Penicillium expansum.

    Science.gov (United States)

    Julca, Irene; Droby, Samir; Sela, Noa; Marcet-Houben, Marina; Gabaldón, Toni

    2015-12-14

    Penicillium digitatum and Penicillium expansum are two closely related fungal plant pathogens causing green and blue mold in harvested fruit, respectively. The two species differ in their host specificity, being P. digitatum restricted to citrus fruits and P. expansum able to infect a wide range of fruits after harvest. Although host-specific Penicillium species have been found to have a smaller gene content, it is so far unclear whether these different host specificities impact genome variation at the intraspecific level. Here we assessed genome variation across four P. digitatum and seven P. expansum isolates from geographically distant regions. Our results show very high similarity (average 0.06 SNPs [single nucleotide polymorphism] per kb) between globally distributed isolates of P. digitatum pointing to a recent expansion of a single lineage. This low level of genetic variation found in our samples contrasts with the higher genetic variability observed in the similarly distributed P. expansum isolates (2.44 SNPs per kb). Patterns of polymorphism in P. expansum indicate that recombination exists between genetically diverged strains. Consistent with the existence of sexual recombination and heterothallism, which was unknown for this species, we identified the two alternative mating types in different P. expansum isolates. Patterns of polymorphism in P. digitatum indicate a recent clonal population expansion of a single lineage that has reached worldwide distribution. We suggest that the contrasting patterns of genomic variation between the two species reflect underlying differences in population dynamics related with host specificities and related agricultural practices. It should be noted, however, that this results should be confirmed with a larger sampling of strains, as new strains may broaden the diversity so far found in P. digitatum.

  2. The γ-gliadin multigene family in common wheat (Triticum aestivum and its closely related species

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    Chen Qing

    2009-04-01

    Full Text Available Abstract Background The unique properties of wheat flour primarily depend on gluten, which is the most important source of protein for human being. γ-Gliadins have been considered to be the most ancient of the wheat gluten family. The complex family structure of γ-gliadins complicates the determination of their function. Moreover, γ-gliadins contain several sets of celiac disease epitopes. However, no systematic research has been conducted yet. Results A total of 170 γ-gliadin genes were isolated from common wheat and its closely related species, among which 138 sequences are putatively functional. The ORF lengths of these sequences range from 678 to 1089 bp, and the repetitive region is mainly responsible for the size heterogeneity of γ-gliadins. The repeat motif P(Q/L/S/T/I/V/R/AF(S/Y/V/Q/I/C/LP(R/L/S/T/H/C/YQ1–2(P(S/L/T/A/F/HQQ1–2is repeated from 7 to 22 times. Sequence polymorphism and linkage disequilibrium analyses show that γ-gliadins are highly diverse. Phylogenic analyses indicate that there is no obvious discrimination between Sitopsis and Ae. tauschii at the Gli-1 loci, compared with diploid wheat. According to the number and placement of cysteine residues, we defined nine cysteine patterns and 17 subgroups. Alternatively, we classified γ-gliadins into two types based on the length of repetitive domain. Amino acid composition analyses indicate that there is a wide range of essential amino acids in γ-gliadins, and those γ-gliadins from subgroup SG-10 and SG-12 and γ-gliadins with a short repetitive domain are more nutritional. A screening of toxic epitopes shows that γ-gliadins with a pattern of C9 and γ-gliadins with a short repetitive domain almost lack any epitopes. Conclusion γ-Gliadin sequences in wheat and closely related Aegilops species are diverse. Each group/subgroup contributes differently to nutritional quality and epitope content. It is suggested that the genes with a short repetitive domain are more

  3. Avian paramyxovirus serotype 3 infection in Neopsephotus, Cyanoramphus, and Neophema species.

    Science.gov (United States)

    Jung, Arne; Grund, Christian; Müller, Inge; Rautenschlein, Silke

    2009-09-01

    An outbreak of avian paramyxovirus serotype 3 (APMV-3) infection occurred in a private bird collection consisting mainly of Neophema species. Two Bourke's parrots (Neopsephotus bourkii) and one red-crowned parakeet (Cyanoramphus novaezelandiae) were examined after developing torticollis and circling. The 3 birds were euthanatized and submitted for necropsy. Brain and liver samples from the 3 birds were homogenized and inoculated into the allantoic cavity of 10-day-old embryonated specific-pathogen-free chicken eggs. An APMV-3 isolate replicated but did not induce embryonic mortality after up to 5 consecutive passages. Allantoic fluid from the second passage was used in hemagglutination testing performed on chicken erythrocytes, which resulted in a titer of 64 hemagglutinating units. Avian paramyxovirus serotype 3 was identified in the allantoic fluid, and a reverse transcription polymerase chain reaction verified the isolate as APMV-3/parakeet. An eventual mortality rate of 70% occurred in the Neophema species, but a group of budgerigars (Melopsittacus undulatus) and parrotlets (Forpus species) kept in the same facility showed no clinical signs during the outbreak.

  4. Relatively recent evolution of pelage coloration in Colobinae: phylogeny and phylogeography of three closely related langur species.

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    Zhijin Liu

    Full Text Available To understand the evolutionary processes leading to the diversity of Asian colobines, we report here on a phylogenetic, phylogeographical and population genetic analysis of three closely related langurs, Trachypithecus francoisi, T. poliocephalus and T. leucocephalus, which are all characterized by different pelage coloration predominantly on the head and shoulders. Therefore, we sequenced a 395 bp long fragment of the mitochondrial control region from 178 T. francoisi, 54 T. leucocephalus and 19 T. poliocephalus individuals, representing all extant populations of these three species. We found 29 haplotypes in T. francoisi, 12 haplotypes in T. leucocephalus and three haplotypes in T. poliocephalus. T. leucocephalus and T. poliocephalus form monophyletic clades, which are both nested within T. francoisi, and diverged from T. francoisi recently, 0.46-0.27 (T. leucocephalus and 0.50-0.25 million years ago (T. poliocephalus. Thus, T. francoisi appears as a polyphyletic group, while T. leucocephalus and T. poliocephalus are most likely independent descendents of T. francoisi that are both physically separated from T. francoisi populations by rivers, open sea or larger habitat gaps. Since T. francoisi populations show no variability in pelage coloration, pelage coloration in T. leucocephalus and T. poliocephalus is most likely the result of new genetic mutations after the split from T. francoisi and not of the fixation of different characters derived from an ancestral polymorphism. This case study highlights that morphological changes for example in pelage coloration can occur in isolated populations in relatively short time periods and it provides a solid basis for studies in related species. Nevertheless, to fully understand the evolutionary history of these three langur species, nuclear loci should be investigated as well.

  5. Drug-induced Hypersensitivity Syndrome Associated with a Marked Increase in Anti-paramyxovirus Antibody Titers in a Scleroderma Patient

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    Taio Naniwa

    2007-01-01

    Discussion: These findings suggest that paramyxovirus infection had contributed to the development of DIHS in this patient and that there is a need to seek evidence of other viral infections in some cases of DIHS, especially those without herpes virus reactivation/infection.

  6. Site of cleavage in infected cells and polypeptides of representative paramyxoviruses grown in cultured cells of the chorioallantoic membrane

    Energy Technology Data Exchange (ETDEWEB)

    Seto, J.T.; Garten, W.; Rott, R. (Giessen Univ. (Germany, F.R.))

    1981-01-01

    Cultured cells of the chorioallantoic membrane (CAM) fulfilled the need of using the same cell system that was permissive for representative paramyxoviruses to carry out studies on the biosynthesis of their glycoproteins in infected cells. The polypeptide composition of the respective paramyxoviruses (Newcastle disease virus (NDV), paramyxovirus Yucaipa (PMY), and Sendai virus), grown in eggs and CAM-cells, was essentially identical. In egg-grown PMY a large glycoprotein (LGP) was present but only in some CAM-grown preparations of virus labeled with (/sup 3/H)-glucosamine and rarely in (/sup 35/S)-methionine or (/sup 3/H)-amino acids (valine, leucine, and tyrosine) labeled viruses. The site of cleavage of precursor F/sub 0/ to Fsub(1,2) was not the same. In contrast to the cleavage of Sendai virus glycoprotein, cleavage was intracellular in NDV and PMY infected cells. Homologous antisera against the glycoproteins failed to inhibit cleavage of HN/sub 0/ or F/sub 0/ in cells infected with the representative paramyxoviruses.

  7. Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China.

    Science.gov (United States)

    Chen, Juan; Zhao, Jietang; Erickson, David L; Xia, Nianhe; Kress, W John

    2015-03-01

    The genus Curcuma L. is commonly used as spices, medicines, dyes and ornamentals. Owing to its economic significance and lack of clear-cut morphological differences between species, this genus is an ideal case for developing DNA barcodes. In this study, four chloroplast DNA regions (matK, rbcL, trnH-psbA and trnL-F) and one nuclear region (ITS2) were generated for 44 Curcuma species and five species from closely related genera, represented by 96 samples. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in matK (89.7%), rbcL (100%), trnH-psbA (100%), trnL-F (95.7%) and ITS2 (82.6%) regions. The results further showed that four candidate chloroplast barcoding regions (matK, rbcL, trnH-psbA and trnL-F) yield no barcode gaps, indicating that the genus Curcuma represents a challenging group for DNA barcoding. The ITS2 region presented large interspecific variation and provided the highest correct identification rates (46.7%) based on BLASTClust method among the five regions. However, the ITS2 only provided 7.9% based on NJ tree method. An increase in discriminatory power needs the development of more variable markers. © 2014 John Wiley & Sons Ltd.

  8. Isolation and characterization of five lytic bacteriophages infecting a Vibrio strain closely related to Vibrio owensii.

    Science.gov (United States)

    Yu, Yan-Ping; Gong, Ting; Jost, Günter; Liu, Wen-Hua; Ye, De-Zan; Luo, Zhu-Hua

    2013-11-01

    Vibrio owensii is a potential bacterial pathogen in marine aquaculture system. In this study, five lytic phages specific against Vibrio strain B8D, closely related to V. owensii, were isolated from seawater of an abalone farm. The phages were characterized with respect to morphology, genome size, growth phenotype, as well as thermal, and pH stability. All phages were found to belong to the family Siphoviridae with long noncontractile tails and terminal fibers. Restriction analysis indicated that the five phages were dsDNA viruses with molecular weights ranging from c. 30 to 48 kb. One-step growth experiments revealed that the phages were heterogeneous in latent periods (10-70 min), rise periods (40-70 min), and burst sizes [23-331 plaque-forming units (PFU) per infected cell] at the same host strain. All phages were thermal stable and were tolerant to a wide range of pH. The results indicated that these phages could be potential candidates of a phage cocktail for biological control of V. owensii in aquaculture systems.

  9. Host plant use among closely related Anaea butterfly species (Lepidoptera, Nymphalidae, Charaxinae

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    J. M. QUEIROZ

    Full Text Available There is a great number of Charaxinae (Lepidoptera: Nymphalidae species in the tropics whose larvae feed on several plant families. However the genus Anaea is almost always associated with Croton species (Euphorbiaceae. This work describes patterns of host plant use by immature and adult abundance on different vertical strata of sympatric Anaea species in a forest of Southeastern Brazil. Quantitative samples of leaves were taken in April/1999 and May/2000 to collect eggs and larvae of four Anaea species on C.alchorneicarpus, C. floribundus and C. salutaris in a semideciduous forest. Sampled leaves were divided into three classes of plant phenological stage: saplings, shrubs and trees. The results showed that the butterfly species are segregating in host plant use on two scales: host plant species and plant phenological stages. C. alchorneicarpus was used by only one Anaea species, whereas C. floribundus was used by three species and C. salutaris by four Anaea species. There was one Anaea species concentrated on sapling, another on sapling/shrub and two others on shrub/tree leaves. Adults of Anaea were more frequent at canopy traps but there were no differences among species caught in traps at different vertical positions. This work supplements early studies on host plant use among Charaxinae species and it describes how a guild of closely related butterfly species may be organized in a complex tropical habitat.

  10. Comparison of song frequency and receptor tuning in two closely related bushcricket species.

    Science.gov (United States)

    Kalmring, K; Rössler, W; Jatho, M; Hoffmann, E

    1995-01-01

    The songs and the structure and physiology of the auditory organs in the closely related bushcricket species Tettigonia viridissima and Tettigonia cantans were investigated comparatively using bioacoustical, histological and neurophysiological methods. The morphology of the crista acustica, the main auditory receptor organ, is very similar in the two species in respect to both the distribution of scolopidia along the length axis of the crista and the dimensions of corresponding scolopidia and attachment structures. The only obvious difference is that T. viridissima has one more scolopidium in the crista acustica and that the overall length of the crista is by about 50 microns larger than in T. cantans. In contrast, differences were found in the physiology of individual auditory receptor cells. Comparison of the threshold characteristics of all the receptor cells of the crista acustica in both species reveals a differential sensitivity of groups of auditory receptor cells at dominant frequencies of the song. In each species, the sensitivity of auditory receptor cells is method to the energy spectrum of the song. These differences in the physiology can partly be explained by differences in transmission characteristics of the acoustic trachea.

  11. Trehalose 6-phosphate signal is closely related to sorbitol in apple (Malus domestica Borkh. cv. Gala)

    Science.gov (United States)

    Zhang, Wen; Lunn, John E.; Feil, Regina; Wang, Yufei; Zhao, Jingjing; Tao, Hongxia; Zhao, Zhengyang

    2017-01-01

    ABSTRACT Trehalose-6-phosphate (Tre6P) is a precursor of trehalose, which is widespread in nature and greatly influences plant growth and development. Tre6P acts as a signal of carbon availability in many plants, but little is known about the function of Tre6P in rosaceous plants, which have specific sorbitol biosynthesis and transportation pathways. In the present study, Tre6P levels and Sorbitol:Tre6P ratios were analyzed in apple (Malus domestica, Borkh. cv. Gala). Tre6P levels were positively correlated with sorbitol content but negatively correlated with sucrose, glucose, and fructose content in developing fruit. However, under sorbitol-limited conditions, Tre6P levels were positively correlated with both sorbitol and sucrose. In the presence of different exogenous sugar supply, Tre6P levels increased corresponding with sorbitol, but this was not the case with sucrose. In addition, Tre6P content and sorbitol:Tre6P ratios were more highly correlated with ADP-glucose levels under sorbitol-limited conditions and fruit development stages, respectively. These results suggest that Tre6P is more closely related to sorbitol than other soluble sugars and has an important role in influencing carbon metabolism in apple. PMID:28069587

  12. Aspergillus oerlinghausenensis, a new mould species closely related to A. fumigatus.

    Science.gov (United States)

    Houbraken, Jos; Weig, Michael; Groß, Uwe; Meijer, Martin; Bader, Oliver

    2016-02-01

    Two isolates belonging to Aspergillus section Fumigati were recovered from German soil on itraconazole containing agar media. Phylogenetic analysis and phenotypic characterization of both isolates show that they represent a novel species named Aspergillus oerlinghausenensis (holotype CBS H-22119(HT), ex-type CBS 139183(T) = IBT 33878 = DTO 316-A3). The species is phylogenetically related to A. fischeri and A. fumigatus. Aspergillus oerlinghausenensis can be differentiated from A. fischeri by its higher growth rate at 50°C. Furthermore, A. oerlinghausenensis is protoheterothallic as only the MAT1-1 idiomorph was detected, while A. fischeri is homothallic. The species differs from A. fumigatus by a weak sporulation on malt extract agar at 25°C, a floccose colony texture on Czapek yeast extract agar and malt extract agar and subglobose instead of subclavate vesicles. The cyp51A promoter region of A. oerlinghausenensis deviates from the previously reported cyp51A promoter regions in A. fumigatus and potentially presents a novel azole resistance conferring modification. Due to the close relationship of A. oerlinghausenensis with A. fischeri and A. fumigatus, this species is placed in a good position for comparative studies involving these species.

  13. Differences in metabolic costs of terrestrial mobility in two closely related species of albatross.

    Science.gov (United States)

    Kabat, Alexander P; Phillips, Richard A; Croxall, John P; Butler, Patrick J

    2007-08-01

    Black-browed albatrosses Thalassarche melanophrys typically colonise steeper habitats than grey-headed albatrosses T. chrysostoma. The present study investigated the effect of colony philopatry on terrestrial locomotory ability in these two species, to determine: (1) if there is a difference in terrestrial locomotory ability between these two closely related species, and (2) what physiological or behavioural adaptations may account for any differences identified. We examined the metabolic cost, mechanical efficiency on an incline, and gait characteristics of terrestrial locomotion of these two species on both level and inclined planes. T. chrysostoma were able to perform at a significantly greater speed than T. melanophrys without reaching a significantly different maximal rate of oxygen consumption (V(O(2))). Conversely, T. melanophrys were able to move up a significantly steeper incline than T. chrysostoma while maintaining a similar maximal V(O(2)). Each species demonstrates stride length, force production (behavioural) and leg length (morphological) adaptations that minimise the cost of traversing their chosen colonies, indicating a clear relationship between terrestrial performance and local topography. However, it is not possible to determine if the difference in locomotory ability results from differences in colony topography, or if choice of colony site is dictated by the ability of the species to traverse different terrain.

  14. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.

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    Robert K Bradley

    2010-03-01

    Full Text Available Changes in gene expression play an important role in evolution, yet the molecular mechanisms underlying regulatory evolution are poorly understood. Here we compare genome-wide binding of the six transcription factors that initiate segmentation along the anterior-posterior axis in embryos of two closely related species: Drosophila melanogaster and Drosophila yakuba. Where we observe binding by a factor in one species, we almost always observe binding by that factor to the orthologous sequence in the other species. Levels of binding, however, vary considerably. The magnitude and direction of the interspecies differences in binding levels of all six factors are strongly correlated, suggesting a role for chromatin or other factor-independent forces in mediating the divergence of transcription factor binding. Nonetheless, factor-specific quantitative variation in binding is common, and we show that it is driven to a large extent by the gain and loss of cognate recognition sequences for the given factor. We find only a weak correlation between binding variation and regulatory function. These data provide the first genome-wide picture of how modest levels of sequence divergence between highly morphologically similar species affect a system of coordinately acting transcription factors during animal development, and highlight the dominant role of quantitative variation in transcription factor binding over short evolutionary distances.

  15. A chestnut seed cystatin differentially effective against cysteine proteinases from closely related pests.

    Science.gov (United States)

    Pernas, M; Sánchez-Monge, R; Gómez, L; Salcedo, G

    1998-12-01

    Cystatin CsC, a cysteine proteinase inhibitor from chestnut (Castanea sativa) seeds, has been purified and characterized. Its full-length cDNA clone was isolated from an immature chestnut cotyledon library. The inhibitor was expressed in Escherichia coli and purified from bacterial extracts. Identity of both seed and recombinant cystatin was confirmed by matrix-assisted laser desorption/ionization mass spectrometry analysis, two-dimensional electrophoresis and N-terminal sequencing. CsC has a molecular mass of 11,275 Da and pI of 6.9. Its amino acid sequence includes all three motifs that are thought to be essential for inhibitory activity, and shows significant identity to other phytocystatins, especially that of cowpea (70%). Recombinant CsC inhibited papain (Ki 29 nM), ficin (Ki 65 nM), chymopapain (Ki 366 nM), and cathepsin B (Ki 473 nM). By contrast with most cystatins, it was also effective towards trypsin (Ki 3489 nM). CsC is active against digestive proteinases from the insect Tribolium castaneum and the mite Dermatophagoides farinae, two important agricultural pests. Its effects on the cysteine proteinase activity of two closely related mite species revealed the high specificity of the chestnut cystatin.

  16. Characterisation of a virus from Australia that is closely related to papaya mosaic potexvirus.

    Science.gov (United States)

    Geering, A D; Thomas, J E

    1999-01-01

    We have isolated a previously undescribed potexvirus from Alternanthera pungens (Amaranthaceae) in southern Queensland, Australia. This virus was shown to have a moderately wide experimental host range, infecting plants in nine of the twelve families tested. Using specific antibodies, a plate trapped antigen ELISA was developed, allowing detection of virions down to 0.8 microgram/ml of leaf extract. Virions averaged 554 nm long and had a capsid protein with a M(r) of 23.1 x 10(3). A portion of the genome containing the capsid protein ORF and 3' untranslated region was cloned and sequenced. From both serological and amino acid sequence comparisons, the virus was shown to be closely related to papaya mosaic potexvirus (PMV). To determine the taxonomic status of the virus, we assessed variation in the amino acid sequence of capsid proteins of distinct species within the potexvirus genus, as well as variation between strains of the same virus. When the core region of the capsid proteins were compared, distinct species had a maximum of 62.2% sequence identity, whereas strains had a minimum of 88.8% identity. By comparison, the core region of the capsid proteins of the Alternanthera virus and PMV had 79.8% identity. We have concluded that the Alternanthera virus is a different species from PMV, and its relationship with PMV resembles that of potyvirus subgroup members.

  17. Creep performance of PVC aged at temperature relatively close to glass transition temperature

    Institute of Scientific and Technical Information of China (English)

    Zhi-hong ZHOU; Yao-long HE; Hong-jiu HU; Feng ZHAO; Xiao-long ZHANG

    2012-01-01

    In order to predict the mechanical performance of the polyvinyl chloride (PVC) at a high operating temperature,a series of short-term tensile creep tests (onetenth of the physical aging time) of the PVC are carried out at 63 ℃ with a small constant stress by a dynamic mechanical analyzer (DMA).The Struik-Kohlrausch (SK)formula and Struik shifting methods are used to describe these creep data for various physical aging time.A new phenomenological model based on the multiple relaxation mechanisms of an amorphous polymer is developed to quantitatively characterize the SK parameters (the initial creep compliance,the characteristic retardation time,and the shape factor) determined by the aging time.It is shown that the momentary creep compliance curve of the PVC at 63 ℃ can be very well fitted by the SK formula for each aging time.However,the SK parameters for the creep curves are not constant during the aging process at the elevated temperatures,and the evolution of these parameters and the creep rate versus aging time curves at the double logarithmic coordinates have shown a nonlinear phenomenon. Moreover,the creep master curves obtained by the superposition with the Struik shifting methods are unsatisfactory in such a case.Finally,the predicted results calculated from the present model incorporating with the SK formula are in excellent agreement with the creep experimental data for the PVC isothermally aged at the temperature relatively close to the glass transition temperature.

  18. New Atglistatin closely related analogues: Synthesis and structure-activity relationship towards adipose triglyceride lipase inhibition.

    Science.gov (United States)

    Roy, Pierre-Philippe; D'Souza, Kenneth; Cuperlovic-Culf, Miroslava; Kienesberger, Petra C; Touaibia, Mohamed

    2016-08-01

    Adipose Triglyceride Lipase (ATGL) performs the first and rate-limiting step in lipolysis by hydrolyzing triacylglycerols stored in lipid droplets to diacylglycerols. By mediating lipolysis in adipose and non-adipose tissues, ATGL is a major regulator of overall energy metabolism and plasma lipid levels. Since chronically high levels of plasma lipids are linked to metabolic disorders including insulin resistance and type 2 diabetes, ATGL is an interesting therapeutic target. In the present study, fourteen closely related analogues of Atglistatin (1), a newly discovered ATGL inhibitor, were synthesized, and their ATGL inhibitory activity was evaluated. The effect of these analogues on lipolysis in 3T3-L1 adipocytes clearly shows that inhibition of the enzyme by Atglistatin (1) is due to the presence of the carbamate and N,N-dimethyl moieties on the biaryl central core at meta and para position, respectively. Mono carbamate-substituted analogue C2, in which the carbamate group was in the meta position as in Atglistatin (1), showed slight inhibition. Low dipole moment of Atglistatin (1) compared to the synthesized analogues possibly explains the lower inhibitory activities.

  19. Host plant use among closely related Anaea butterfly species (Lepidoptera, Nymphalidae, Charaxinae

    Directory of Open Access Journals (Sweden)

    QUEIROZ J. M.

    2002-01-01

    Full Text Available There is a great number of Charaxinae (Lepidoptera: Nymphalidae species in the tropics whose larvae feed on several plant families. However the genus Anaea is almost always associated with Croton species (Euphorbiaceae. This work describes patterns of host plant use by immature and adult abundance on different vertical strata of sympatric Anaea species in a forest of Southeastern Brazil. Quantitative samples of leaves were taken in April/1999 and May/2000 to collect eggs and larvae of four Anaea species on C.alchorneicarpus, C. floribundus and C. salutaris in a semideciduous forest. Sampled leaves were divided into three classes of plant phenological stage: saplings, shrubs and trees. The results showed that the butterfly species are segregating in host plant use on two scales: host plant species and plant phenological stages. C. alchorneicarpus was used by only one Anaea species, whereas C. floribundus was used by three species and C. salutaris by four Anaea species. There was one Anaea species concentrated on sapling, another on sapling/shrub and two others on shrub/tree leaves. Adults of Anaea were more frequent at canopy traps but there were no differences among species caught in traps at different vertical positions. This work supplements early studies on host plant use among Charaxinae species and it describes how a guild of closely related butterfly species may be organized in a complex tropical habitat.

  20. Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species.

    Science.gov (United States)

    Kanzi, Aquillah Mumo; Wingfield, Brenda Diana; Steenkamp, Emma Theodora; Naidoo, Sanushka; van der Merwe, Nicolaas Albertus

    2016-01-01

    In this study, the complete mitochondrial (mt) genomes of Chrysoporthe austroafricana (190,834 bp), C. cubensis (89,084 bp) and C. deuterocubensis (124,412 bp) were determined. Additionally, the mitochondrial genome of another member of the Cryphonectriaceae, namely Cryphonectria parasitica (158,902 bp), was retrieved and annotated for comparative purposes. These genomes showed high levels of synteny, especially in regions including genes involved in oxidative phosphorylation and electron transfer, unique open reading frames (uORFs), ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as intron positions. Comparative analyses revealed signatures of duplication events, intron number and length variation, and varying intronic ORFs which highlighted the genetic diversity of mt genomes among the Cryphonectriaceae. These mt genomes showed remarkable size polymorphism. The size polymorphism in the mt genomes of these closely related Chrysoporthe species was attributed to the varying number and length of introns, coding sequences and to a lesser extent, intergenic sequences. Compared to publicly available fungal mt genomes, the C. austroafricana mt genome is the second largest in the Ascomycetes thus far.

  1. Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution.

    Directory of Open Access Journals (Sweden)

    Jonathan eFilée

    2015-06-01

    Full Text Available Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales. Origin and evolution of these Giant Viruses (GVs remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for 5 groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no trend of genome expansion or general tendency of genome contraction. Instead, GV genomes accumulated genomic mutations over the time with gene gains compensating the different losses. In addition, each lineage displays specific patterns of genome evolution. Mimiviridae (megaviruses and mimiviruses and Chlorella Phycodnaviruses evolved mainly by duplications and losses of genes belonging to large paralogous families (including movements of diverse mobiles genetic elements, whereas Micromonas and Ostreococcus Phycodnaviruses derive most of their genetic novelties thought lateral gene transfers. Taken together, these data support an accordion-like model of evolution in which GV genomes have undergone successive steps of gene gain and gene loss, accrediting the hypothesis that genome gigantism appears early, before the diversification of the different GV lineages.

  2. Trehalose 6-phosphate signal is closely related to sorbitol in apple (Malus domestica Borkh. cv. Gala

    Directory of Open Access Journals (Sweden)

    Wen Zhang

    2017-02-01

    Full Text Available Trehalose-6-phosphate (Tre6P is a precursor of trehalose, which is widespread in nature and greatly influences plant growth and development. Tre6P acts as a signal of carbon availability in many plants, but little is known about the function of Tre6P in rosaceous plants, which have specific sorbitol biosynthesis and transportation pathways. In the present study, Tre6P levels and Sorbitol:Tre6P ratios were analyzed in apple (Malus domestica, Borkh. cv. Gala. Tre6P levels were positively correlated with sorbitol content but negatively correlated with sucrose, glucose, and fructose content in developing fruit. However, under sorbitol-limited conditions, Tre6P levels were positively correlated with both sorbitol and sucrose. In the presence of different exogenous sugar supply, Tre6P levels increased corresponding with sorbitol, but this was not the case with sucrose. In addition, Tre6P content and sorbitol:Tre6P ratios were more highly correlated with ADP-glucose levels under sorbitol-limited conditions and fruit development stages, respectively. These results suggest that Tre6P is more closely related to sorbitol than other soluble sugars and has an important role in influencing carbon metabolism in apple.

  3. Relational Systems: How Older Women with Chronic Health Problems Construct Close Relationships

    Science.gov (United States)

    McCann, Brandy Renee; Roberto, Karen A.

    2012-01-01

    Close relationships are important throughout life, but their dynamics may change as chronic health conditions permeate the lives of older women. To understand how older women (N = 36) manage their close relationships, this study was guided by two research questions: How do older women with chronic health conditions define meaningful relationships?…

  4. Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park.

    Science.gov (United States)

    Romano, Christine; D'Imperio, Seth; Woyke, Tanja; Mavromatis, Konstantinos; Lasken, Roger; Shock, Everett L; McDermott, Timothy R

    2013-05-01

    We describe the complete genome sequences of four closely related Hydrogenobaculum sp. isolates (≥ 99.7% 16S rRNA gene identity) that were isolated from the outflow channel of Dragon Spring (DS), Norris Geyser Basin, in Yellowstone National Park (YNP), WY. The genomes range in size from 1,552,607 to 1,552,931 bp, contain 1,667 to 1,676 predicted genes, and are highly syntenic. There are subtle differences among the DS isolates, which as a group are different from Hydrogenobaculum sp. strain Y04AAS1 that was previously isolated from a geographically distinct YNP geothermal feature. Genes unique to the DS genomes encode arsenite [As(III)] oxidation, NADH-ubiquinone-plastoquinone (complex I), NADH-ubiquinone oxidoreductase chain, a DNA photolyase, and elements of a type II secretion system. Functions unique to strain Y04AAS1 include thiosulfate metabolism, nitrate respiration, and mercury resistance determinants. DS genomes contain seven CRISPR loci that are almost identical but are different from the single CRISPR locus in strain Y04AAS1. Other differences between the DS and Y04AAS1 genomes include average nucleotide identity (94.764%) and percentage conserved DNA (80.552%). Approximately half of the genes unique to Y04AAS1 are predicted to have been acquired via horizontal gene transfer. Fragment recruitment analysis and marker gene searches demonstrated that the DS metagenome was more similar to the DS genomes than to the Y04AAS1 genome, but that the DS community is likely comprised of a continuum of Hydrogenobaculum genotypes that span from the DS genomes described here to an Y04AAS1-like organism, which appears to represent a distinct ecotype relative to the DS genomes characterized.

  5. Restricted variation in plant barcoding markers limits identification in closely related bryophyte species.

    Science.gov (United States)

    Hassel, Kristian; Segreto, Rossana; Ekrem, Torbjørn

    2013-11-01

    Species-level identification and delimitation of bryophytes using the proposed general barcode markers for land plants has been challenging. Bryophyta (mosses) is the second most species-rich group of land plants after angiosperms, and it is thus of great importance to find useful barcoding regions also for this group of plants. We investigated how the plastid regions atpF-atpH, rbcL and trnH-psbA and the nuclear ITS2 region performed as barcode markers on closely related bryophyte taxa of selected moss (Bartramia, Distichium, Fissidens, Meesia and Syntrichia) and liverwort (Blepharostoma) genera from boreal and arctic regions. We also evaluated how sequencing success of herbarium specimens is related to length of the sequenced fragment, specimen age and taxonomic group. Sequencing success was higher for shorter fragments and younger herbarium specimens, but was lower than expected in the genera Distichium and Fissidens, indicating imperfect universality of the primers used. None of the studied DNA barcode regions showed a consistent barcode gap across the studied genera. As a single locus, the region atpF-atpH performed slightly better than rbcL and ITS2 and much better than trnH-psbA in terms of grouping conspecific sequences in monophyletic groups. This marker also gave a higher percentage of correct hits when conducting blast searches on a local database of identified sequences. Concatenated data sets of two and three markers grouped more conspecific sequences in monophyletic groups, but the improvement was not great compared with atpF-atpH alone. A discussion of recent studies testing barcode regions for bryophytes is given. We conclude that atpF-atpH, rbcL and ITS2 are to be the most promising barcode markers for mosses.

  6. Chloroplast gene arrangement variation within a closely related group of green algae (Trebouxiophyceae, Chlorophyta).

    Science.gov (United States)

    Letsch, Molly R; Lewis, Louise A

    2012-09-01

    The 22 published chloroplast genomes of green algae, representing sparse taxonomic sampling of diverse lineages that span over one billion years of evolution, each possess a unique gene arrangement. In contrast, many of the >190 published embryophyte (land plant) chloroplast genomes have relatively conserved architectures. To determine the phylogenetic depth at which chloroplast gene rearrangements occur in green algae, a 1.5-4 kb segment of the chloroplast genome was compared across nine species in three closely related genera of Trebouxiophyceae (Chlorophyta). In total, four distinct gene arrangements were obtained for the three genera Elliptochloris, Hemichloris, and Coccomyxa. In Elliptochloris, three distinct chloroplast gene arrangements were detected, one of which is shared with members of its sister genus Hemichloris. Both species of Coccomyxa examined share the fourth arrangement of this genome region, one characterized by very long spacers. Next, the order of genes found in this segment of the chloroplast genome was compared across green algae and land plants. As taxonomic ranks are not equivalent among different groups of organisms, the maximum molecular divergence among taxa sharing a common gene arrangement in this genome segment was compared. Well-supported clades possessing a single gene order had similar phylogenetic depth in green algae and embryophytes. When the dominant gene order of this chloroplast segment in embryophytes was assumed to be ancestral for land plants, the maximum molecular divergence was found to be over two times greater in embryophytes than in trebouxiophyte green algae. This study greatly expands information about chloroplast genome variation in green algae, is the first to demonstrate such variation among congeneric green algae, and further illustrates the fluidity of green algal chloroplast genome architecture in comparison to that of many embryophytes.

  7. The relation between anorexic symptoms in women and their reports of trustworthiness in interactions with close persons.

    Science.gov (United States)

    Rotenberg, Ken J; Edwards, Kelley

    2017-08-01

    The study examined the relation between women's anorexic symptoms and their reports of trustworthiness in interactions with close persons. Ninety-eight females (mean age=24years-10months) completed the anorexic symptom subscale of the SEDS and reported (ascribed) the extent to which they showed reliability, emotional, and honesty trustworthiness behaviors in interactions with their mother, father, and close friend. Negative linear relations were found between anorexic symptoms and ascribed: (a) trustworthiness with close friends; (b) reliability trustworthiness; and (c) at a trend level, honesty trustworthiness. These were qualified by curvilinear relations and by elevated anorexic vs normative group comparisons. It was found that women with elevated anorexic symptoms ascribed lower trustworthiness than did women with the normal range of anorexic symptoms. The findings were interpreted as supporting the conclusion that women with elevated levels of anorexic symptoms are inclined to believe that they are deceptive in their interactions with close persons, primarily friends. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. A hetero-micro-seeding strategy for readily crystallizing closely related protein variants.

    Science.gov (United States)

    Islam, Mohammad M; Kuroda, Yutaka

    2017-09-01

    Protein crystallization remains difficult to rationalize and screening for optimal crystallization conditions is a tedious and time consuming procedure. Here, we report a hetero-micro-seeding strategy for producing high resolution crystals of closely related protein variants, where micro crystals from a readily crystallized variant are used as seeds to develop crystals of other variants less amenable to crystallization. We applied this strategy to Bovine Pancreatic Trypsin Inhibitor (BPTI) variants, which would not crystallize using standard crystallization practice. Out of six variants in our analysis, only one called BPTI-[5,55]A14G formed well behaving crystals; and the remaining five (A14GA38G, A14GA38V, A14GA38L, A14GA38I, and A14GA38K) could be crystallized only using micro-seeds from the BPTI-[5,55]A14G crystal. All hetero-seeded crystals diffracted at high resolution with minimum mosaicity, retaining the same space group and cell dimension. Moreover, hetero-micro-seeding did not introduce any biases into the mutant's structure toward the seed structure, as demonstrated by A14GA38I structures solved using micro-seeds from A14GA38G, A14GA38L and A14GA38I. Though hetero-micro-seeding is a simple and almost naïve strategy, this is the first direct demonstration of its workability. We believe that hetero-micro-seeding, which is contrasting with the popular idea that crystallization requires highly purified proteins, could contribute a new tool for rapidly solving protein structures in mutational analysis studies. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Different patterns of oviposition learning in two closely related ectoparasitoid wasps with contrasting reproductive strategies

    Science.gov (United States)

    Sasakawa, Kôji; Uchijima, Kenta; Shibao, Harunobu; Shimada, Masakazu

    2013-02-01

    Many parasitoid wasps learn host-associated cues and use them in subsequent host-searching behavior. This associative learning, namely "oviposition learning," has been investigated in many studies. However, few studies have compared multiple species, and no comparative study has previously been conducted on ectoparasitoid species. We compared the effects of oviposition learning on host preference and offspring sex ratio in two closely related ectoparasitoid wasps with contrasting reproductive strategies, Anisopteromalus calandrae (r-strategist) and its sibling species (K-strategist). Using two bruchine hosts, Callosobruchus chinensis and Callosobruchus maculatus larvae infesting the cowpea Vigna unguiculata, oviposition choice experiments were performed at high and low host densities. In both species, no conspicuous effect on the offspring sex ratio was detected, but effects on host preference were found to differ between the species. In A. calandrae, the effects were detected only at high host density, suggesting that oviposition learning plays a role in host discrimination from a short distance but not from a long distance. In the sibling species, those effects were not detected in any of the cases, suggesting the absence of oviposition learning. These results are compatible with those of previous comparative studies of endoparasitoid wasps in that few lifetime oviposition experiences and/or low reward per foraging decision result in low or absent oviposition learning ability. This finding may indicate that ecological traits contributing to learning ability are similar between endoparasitoid and ectoparasitoid wasps. Thus, our species comparison of ectoparasitoids provides another model system for investigating learning and memory dynamics in parasitoid wasps.

  10. Different patterns of oviposition learning in two closely related ectoparasitoid wasps with contrasting reproductive strategies.

    Science.gov (United States)

    Sasakawa, Kôji; Uchijima, Kenta; Shibao, Harunobu; Shimada, Masakazu

    2013-02-01

    Many parasitoid wasps learn host-associated cues and use them in subsequent host-searching behavior. This associative learning, namely "oviposition learning," has been investigated in many studies. However, few studies have compared multiple species, and no comparative study has previously been conducted on ectoparasitoid species. We compared the effects of oviposition learning on host preference and offspring sex ratio in two closely related ectoparasitoid wasps with contrasting reproductive strategies, Anisopteromalus calandrae (r-strategist) and its sibling species (K-strategist). Using two bruchine hosts, Callosobruchus chinensis and Callosobruchus maculatus larvae infesting the cowpea Vigna unguiculata, oviposition choice experiments were performed at high and low host densities. In both species, no conspicuous effect on the offspring sex ratio was detected, but effects on host preference were found to differ between the species. In A. calandrae, the effects were detected only at high host density, suggesting that oviposition learning plays a role in host discrimination from a short distance but not from a long distance. In the sibling species, those effects were not detected in any of the cases, suggesting the absence of oviposition learning. These results are compatible with those of previous comparative studies of endoparasitoid wasps in that few lifetime oviposition experiences and/or low reward per foraging decision result in low or absent oviposition learning ability. This finding may indicate that ecological traits contributing to learning ability are similar between endoparasitoid and ectoparasitoid wasps. Thus, our species comparison of ectoparasitoids provides another model system for investigating learning and memory dynamics in parasitoid wasps.

  11. Rapid identification of closely related muscle foods by vibrational spectroscopy and machine learning.

    Science.gov (United States)

    Ellis, David I; Broadhurst, David; Clarke, Sarah J; Goodacre, Royston

    2005-12-01

    Muscle foods are an integral part of the human diet and during the last few decades consumption of poultry products in particular has increased significantly. It is important for consumers, retailers and food regulatory bodies that these products are of a consistently high quality, authentic, and have not been subjected to adulteration by any lower-grade material either by accident or for economic gain. A variety of methods have been developed for the identification and authentication of muscle foods. However, none of these are rapid or non-invasive, all are time-consuming and difficulties have been encountered in discriminating between the commercially important avian species. Whilst previous attempts have been made to discriminate between muscle foods using infrared spectroscopy, these have had limited success, in particular regarding the closely related poultry species, chicken and turkey. Moreover, this study includes novel data since no attempts have been made to discriminate between both the species and the distinct muscle groups within these species, and this is the first application of Raman spectroscopy to the study of muscle foods. Samples of pre-packed meat and poultry were acquired and FT-IR and Raman measurements taken directly from the meat surface. Qualitative interpretation of FT-IR and Raman spectra at the species and muscle group levels were possible using discriminant function analysis. Genetic algorithms were used to elucidate meaningful interpretation of FT-IR results in (bio)chemical terms and we show that specific wavenumbers, and therefore chemical species, were discriminatory for each type (species and muscle) of poultry sample. We believe that this approach would aid food regulatory bodies in the rapid identification of meat and poultry products and shows particular potential for rapid assessment of food adulteration.

  12. Active ammonia oxidizers in an acidic soil are phylogenetically closely related to neutrophilic archaeon.

    Science.gov (United States)

    Wang, Baozhan; Zheng, Yan; Huang, Rong; Zhou, Xue; Wang, Dongmei; He, Yuanqiu; Jia, Zhongjun

    2014-03-01

    All cultivated ammonia-oxidizing archaea (AOA) within the Nitrososphaera cluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence of Nitrososphaera-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth of Nitrososphaera-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of amoA genes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the "heavy" DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that (13)CO2 assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both (13)C-labeled amoA and 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strains Nitrososphaera viennensis EN76 and JG1 within the Nitrososphaera cluster. Our results provide strong evidence for the adaptive growth of Nitrososphaera-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated.

  13. Visual perception can account for the close relation between numerosity processing and computational fluency

    Directory of Open Access Journals (Sweden)

    Xinlin eZhou

    2015-09-01

    Full Text Available Studies have shown that numerosity processing (e.g., comparison of numbers of dots in two dot arrays is significantly correlated with arithmetic performance. Researchers have attributed this association to the fact that both tasks share magnitude processing. The current investigation tested an visual perception hypothesis that visual perceptual ability (as measured by a figure-matching task can account for the close relation between numerosity processing and arithmetic performance (computational fluency. Four hundred and twenty four third- to fifth-grade children (220 boys and 204 girls, 8.0 to 11.0 years old; 120 third graders, 146 fourth graders, and 158 fifth graders were recruited from two schools (one urban and one suburban in Beijing, China. Six classes were randomly selected from each school, and all students in each selected class were asked to participate in the study. All children were given a series of cognitive and mathematical tests, including numerosity comparison, figure matching, forward verbal working memory, visual tracing, non-verbal matrices reasoning, mental rotation, choice reaction time, arithmetic tests and curriculum-based mathematical achievement test. Results showed that figure-matching ability had higher correlations with numerosity processing and computational fluency than did other cognitive factors (e.g., forward verbal working memory, visual tracing, non-verbal matrices reasoning, mental rotation, and choice reaction time. More important, hierarchical multiple regression showed that figure matching ability accounted for the well-established association between numerosity processing and computational fluency. The results suggest that visual perceptual ability, rather than magnitude processing, may be the shared component of numerosity processing and arithmetic performance.

  14. Mammary-type myofibroblastoma of soft tissue: a tumor closely related to spindle cell lipoma.

    Science.gov (United States)

    McMenamin, M E; Fletcher, C D

    2001-08-01

    Mammary myofibroblastoma is a benign breast tumor, with a reported predilection for older men. It is composed of fascicles of spindle cells having features of myofibroblasts, with intervening hyalinized collagenous stroma and a variably prominent component of adipose tissue. The spindle cells characteristically express both CD34 and desmin. Herein, we report the clinicopathologic features of nine tumors that were morphologically and immunohistochemically identical to myofibroblastoma of breast; however, they arose in subcutaneous soft tissue at extramammary sites. The study group comprised seven men and two women with an age range of 35-67 years (median 53 years). Lesions presented as either a slowly growing painless mass or were incidental findings at the time of surgery. The site distribution was as follows: inguinal/groin area (five cases) and one case each in posterior vaginal wall, buttock, anterior abdominal wall, and mid-back. Tumor size ranged from 2 to 13 cm (median 6 cm), and all lesions were well circumscribed. Eight tumors had a component of adipose tissue (ranging from 10% to 60%), within which some variation in adipocyte size was often seen. One case showed epithelioid cytomorphology and three cases showed rare atypical or multinucleated cells. Focal myxoid stromal change was seen in four cases. Tumor cells were positive for desmin (9 of 9 cases), CD34 (8 of 9 cases), and occasionally positive for smooth muscle actin (3 of 9 cases). Lesions were marginally excised with no recurrences to date, although follow-up is very limited. Lesions with morphologic and immunophenotypic features similar to myofibroblastoma of breast can arise at extramammary sites, with an apparent predilection for the inguinal area of older men. Both mammary and extramammary lesions show morphologic overlap with spindle cell lipoma and are likely closely related.

  15. Glycolysis Is Dynamic and Relates Closely to Respiration Rate in Stored Sugarbeet Roots

    Directory of Open Access Journals (Sweden)

    Clarice A. Megguer

    2017-05-01

    storage and that changes in glycolysis are closely related to changes in sugarbeet root respiration.

  16. Identifying mutation regions for closely related individuals without a known pedigree

    Science.gov (United States)

    2012-01-01

    Background Linkage analysis is the first step in the search for a disease gene. Linkage studies have facilitated the identification of several hundred human genes that can harbor mutations leading to a disease phenotype. In this paper, we study a very important case, where the sampled individuals are closely related, but the pedigree is not given. This situation happens very often when the individuals share a common ancestor 6 or more generations ago. To our knowledge, no algorithm can give good results for this case. Results To solve this problem, we first developed some heuristic algorithms for haplotype inference without any given pedigree. We propose a model using the parsimony principle that can be viewed as an extension of the model first proposed by Dan Gusfield. Our heuristic algorithm uses Clark’s inference rule to infer haplotype segments. Conclusions We ran our program both on the simulated data and a set of real data from the phase II HapMap database. Experiments show that our program performs well. The recall value is from 90% to 99% in various cases. This implies that the program can report more than 90% of the true mutation regions. The value of precision varies from 29% to 90%. When the precision is 29%, the size of the reported regions is three times that of the true mutation region. This is still very useful for narrowing down the range of the disease gene location. Our program can complete the computation for all the tested cases, where there are about 110,000 SNPs on a chromosome, within 20 seconds. PMID:22731852

  17. Initial data sets and the topology of closed three-manifolds in general relativity

    Science.gov (United States)

    Carfora, M.

    1983-10-01

    The interaction between the matter content of a closed physical space associated with a generic gravitational configuration and the topology of the underlying closed three-manifold is discussed. Within the context of the conformal approach to the initial value problem, it is shown that the presence of enough matter and radiation favors the three-sphere topology or the worm-hole topology. It is argued that such topologies leave more room for possible gravitational initial data sets for the field equations.

  18. A role of Bradyrhizobium elkanii and closely related strains in the degradation of methoxychlor in soil and surface water environments.

    Science.gov (United States)

    Satsuma, Koji; Masuda, Minoru; Sato, Kiyoshi

    2013-01-01

    We have reported that a leguminous bacterial strain, Bradyrhizobium sp. strain 17-4, isolated from river sediment, phylogenetically very close to Bradyrhizobium elkanii, degraded methoxychlor through O-demethylation and oxidative dechlorination. In the present investigation, we found that B. elkanii (USDA94), a standard species deposited in the Culture Collection, degraded methoxychlor. Furthermore, Bradyrhizobium sp. strain 4-1, also very close to B. elkanii, isolated from Japanese paddy field soil, degraded methoxychlor. These B. elkanii and closely related strains degraded methoxychlor through almost identical metabolic pathways, and cleaved the phenyl ring and mineralized. In contrast, another representative Bradyrhizobium species, B. japonicum (USDA110), did not degrade methoxychlor at all. Based on these findings, B. elkanii and closely related strains are likely to play an important role not only in providing the readily biodegradable substrates but also in completely degrading (mineralizing) methoxychlor by themselves in the soil and surface water environment.

  19. Negative aspects of close social relations and 10-year incident ischaemic heart disease hospitalization among middle-aged Danes

    DEFF Research Database (Denmark)

    Lund, Rikke; Rod, Naja Hulvej; Thielen, Karsten

    2014-01-01

    BACKGROUND: Little is known about the association between negative aspects of close social relations and development of ischaemic heart disease (IHD). We aim to address if the experience of worries/demands and conflicts with close social relations are related to risk of first-time hospitalization...... National Patient Registry. Cox regression analysis was used to analyse data and all analyses were adjusted for age, gender, social class, cohabitation, and depressive symptoms. RESULTS: Worries/demands from and conflicts with children were associated with IHD hospitalization in an exposure-dependent manner...... was found for conflicts with partner. High levels of worries/demands from or conflicts with family and friends were associated with a 40% higher risk of IHD. CONCLUSIONS: Negative aspects of close social relations are associated with higher risk of incident IHD hospitalization except for conflicts...

  20. Assessment of Contemporary Genetic Diversity and Inter-Taxa/Inter-Region Exchange of Avian Paramyxovirus Serotype 1 in Wild Birds Sampled in North America, 1986-2014

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Data set pertaining to avian paramyxovirus (APMV-1) sequences used in phylogenetic analyses. Data contains GenBank Accession numbers, host species common name and...

  1. Complete Genome Sequence of Ehrlichia mineirensis, a Novel Organism Closely Related to Ehrlichia canis with a New Host Association

    OpenAIRE

    Cabezas-Cruz, Alejandro; Zweygarth, Erich; Broniszweska, Marzena; Passos,Lygia M.F.; Ribeiro,Múcio Flávio Barbosa; Manrique, Marina; Tobes,Raquel; de la Fuente, José

    2015-01-01

    We report here the complete genome sequencing of Ehrlichia mineirensis, an Ehrlichia organism that was isolated from the hemolymph of Rhipicephalus microplus–engorged females. E. mineirensis is the best characterized Ehrlichia isolate from a novel cattle-related clade closely related to the monocytotropic pathogen E. canis.

  2. Identification of Traditional She Medicine Shi-Liang Tea Species and Closely Related Species Using the ITS2 Barcode

    Directory of Open Access Journals (Sweden)

    Shuangjiao Ma

    2017-02-01

    Full Text Available Traditional She medicine is part of China’s cultural heritage and has become remarkably popular worldwide. The Shi-Liang tea is made from the processed leaves of Chimonanthus salicifolius S. Y. Hu and Chimonanthus zhejiangensis M. C. Liu. To ensure the safety and efficacy of Shi-Liang tea, we used DNA barcoding based on the internal transcribed spacer 2 (ITS2 of nuclear ribosomal DNA to distinguish the original plant sources of Shi-Liang tea from closely related species. All 71 ITS2 sequences were aligned by Clustal-W, and genetic distances were computed using MEGA 6.0 according to the Kimura 2-parameter model. The results indicated that the sequence lengths of ITS2 regions of the original plants of Shi-Liang tea and closely related species ranged from 256 bp to 260 bp. Interspecific genetic distances ranged from 0 to 0.078. The neighbor-joining (NJ tree showed that the original plants of Shi-Liang tea species can be easily differentiated from closely related species. Distinct molecular differences were found between the secondary structures of ITS2 sequences from Shi-Liang tea and closely related species. The results in the present investigation suggested that the ITS2 could be an effective DNA marker to identify the original plants of Shi-Liang tea and their closely related species. These DNA barcodes can greatly benefit the supervision of the commercial circulation of She medicine.

  3. Domain architecture and oligomerization properties of the paramyxovirus PIV 5 hemagglutinin-neuraminidase (HN) protein.

    Science.gov (United States)

    Yuan, Ping; Leser, George P; Demeler, Borries; Lamb, Robert A; Jardetzky, Theodore S

    2008-09-01

    The mechanism by which the paramyxovirus hemagglutinin-neuraminidase (HN) protein couples receptor binding to activation of virus entry remains to be fully understood, but the HN stalk is thought to play an important role in the process. We have characterized ectodomain constructs of the parainfluenza virus 5 HN to understand better the underlying architecture and oligomerization properties that may influence HN functions. The PIV 5 neuraminidase (NA) domain is monomeric whereas the ectodomain forms a well-defined tetramer. The HN stalk also forms tetramers and higher order oligomers with high alpha-helical content. Together, the data indicate that the globular NA domains form weak intersubunit interactions at the end of the HN stalk tetramer, while stabilizing the stalk and overall oligomeric state of the ectodomain. Electron microscopy of the HN ectodomain reveals flexible arrangements of the NA and stalk domains, which may be important for understanding how these two HN domains impact virus entry.

  4. Characterization of Pigeon Paramyxoviruses (Newcastle disease virus) Isolated in Kazakhstan in 2005

    Institute of Scientific and Technical Information of China (English)

    Andrey Bogoyavlenskiy; Vladimir Berezin; Alexey Prilipov; Eugeniy Usachev; Ilya Korotetskiy; Irina Zaitceva; Aydyn Kydyrmanov; Marat Sayatov

    2012-01-01

    Isolates of Newcastle disease virus (NDV) from deceased wild and domestic pigeons in Kazakhstan were obtained from the Almaty region during 2005 and were genotypically analyzed by using reverse transcription polymerase chain reaction (RT-PCR) with primers specific to the viral fusion (F) protein gene.Part of the amplified F protein DNA product (nucleotide sequence 47-422) and the deduced amino acid sequenceswere compared phylogenetically with those from strains previously reported in other geographic regions.Phylogenetic analysis indicated that the Kazakhstanian pigeon paramyxovirus type 1 (PPMV-1) isolates belong to genotype Ⅵ or 4bii.To our knowledge,this is the first reported Ⅵ isolates that possess the sequences of 112 GKRQKR116* F117 within the F0 protein.The information is fundamental to improving the efficiency of control strategies and vaccine development for NDV.

  5. Structure of the uncleaved ectodomain of the paramyxovirus (hPIV3) fusion protein

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Hsien-Sheng; Paterson, Reay G.; Wen, Xiaolin; Lamb, Robert A.; Jardetzky, Theodore S. (NWU)

    2010-03-08

    Class I viral fusion proteins share common mechanistic and structural features but little sequence similarity. Structural insights into the protein conformational changes associated with membrane fusion are based largely on studies of the influenza virus hemagglutinin in pre- and postfusion conformations. Here, we present the crystal structure of the secreted, uncleaved ectodomain of the paramyxovirus, human parainfluenza virus 3 fusion (F) protein, a member of the class I viral fusion protein group. The secreted human parainfluenza virus 3 F forms a trimer with distinct head, neck, and stalk regions. Unexpectedly, the structure reveals a six-helix bundle associated with the postfusion form of F, suggesting that the anchor-minus ectodomain adopts a conformation largely similar to the postfusion state. The transmembrane anchor domains of F may therefore profoundly influence the folding energetics that establish and maintain a metastable, prefusion state.

  6. Asexual reproduction in a close relative of Arabidopsis: a genetic investigation of apomixis in Boechera ( Brassicaceae).

    NARCIS (Netherlands)

    Schranz, M.E.; Kantama, L.; Jong, de J.H.S.G.M.; Mitchell-Olds, T.

    2006-01-01

    Understanding apomixis (asexual reproduction through seeds) is of great interest to both plant breeders and evolutionary biologists. The genus Boechera is an excellent system for studying apomixis because of its close relationship to Arabidopsis, the occurrence of apomixis at the diploid level, and

  7. Avian paramyxovirus serotype 1 isolates from the spinal cord of parrots display a very low virulence.

    Science.gov (United States)

    Grund, C H; Werner, O; Gelderblom, H R; Grimm, F; Kösters, J

    2002-11-01

    The spinal cord of 32 psittacines suffering from proventricular dilatation disease (PDD) was investigated. In six cases, a virus was isolated which upon electron microscopic examination revealed morphological details typical of members of the Paramyxoviridae. All isolates were subsequently characterized as avian paramyxovirus serotype 1 (APMV-1) by type-specific polyclonal antisera. According to their reactivity with APMV-1 specific monoclonal antibodies, the six isolates shared epitopes within the haemagglutinin-neuraminidase spike protein, distinct from pigeon-type paramyxoviruses and the LaSota vaccine strain. This grouping was further corroborated by properties of the haemagglutinin: all isolates showed a very thermosensitive haemagglutination activity and were rapid eluters. Virulence of the APMV-1 isolates in 1-day-old specific pathogen free (spf) chicken was very low, with intracerebral pathogenicity indices between 0 and 0.1. In embryonated spf chicken eggs, psittacine isolates replicated to high titres (10(8.6)-10(10.7) EID50/ml). However, they exhibited a reduced lethality over an observation time of 7 days (10(6.1)-10(8.3) ELD50/ml). In a haemagglutination inhibition test with parrot sera from birds with no history of APMV-1 vaccination, sera reacted preferentially with two isolates compared with APMV-1 vaccine strains LaSota and B1. The other four isolates exhibited a differentiated reaction pattern with the parrot sera, indicating an antigenic inhomogeneity. This is the first report of isolating very low virulent APMV-1 from neuronal tissue of parrots and implications for a possible role in slow progressing disease will be discussed.

  8. Sustained activation of interferon regulatory factor 3 during infection by paramyxoviruses requires MDA5.

    Science.gov (United States)

    Grandvaux, Nathalie; Guan, Xiaochun; Yoboua, Fabrice; Zucchini, Nicolas; Fink, Karin; Doyon, Priscilla; Martin, Lydie; Servant, Marc J; Chartier, Stéfany

    2014-01-01

    Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are the main cytosolic sensors of single-stranded RNA viruses, including paramyxoviruses, and are required to initiate a quick and robust innate antiviral response. Despite different ligand-binding properties, the consensus view is that RIG-I and MDA5 trigger common signal(s) to activate interferon regulatory factor 3 (IRF-3) and NF-κB, and downstream antiviral and proinflammatory cytokine expression. Here, we performed a thorough analysis of the temporal involvement of RIG-I and MDA5 in the regulation of IRF-3 during respiratory syncytial virus (RSV) infection. Based on specific RNA interference-mediated knockdown of RIG-I and MDA5 in A549 cells, we confirmed that RIG-I is critical for the initiation of IRF-3 phosphorylation, dimerization and downstream gene expression. On the other hand, our experiments yielded the first evidence that knockdown of MDA5 leads to early ubiquitination and proteasomal degradation of active IRF-3. Conversely, ectopic expression of MDA5 prolonged RIG-I-induced IRF-3 activation. Altogether, we provide novel mechanistic insight into the temporal involvement of RIG-I and MDA5 in the innate antiviral response. While RIG-I is essential for initial IRF-3 activation, engagement of induced MDA5 is essential to prevent early degradation of IRF-3, thereby sustaining IRF-3-dependent antiviral gene expression. MDA5 plays a similar role during Sendai virus infection suggesting that this model is not restricted to RSV amongst paramyxoviruses.

  9. A modified nodal pressure method for calculating flow distribution in hydraulic circuits for the case of unconventional closing relations

    Directory of Open Access Journals (Sweden)

    Egor M. Mikhailovsky

    2015-06-01

    Full Text Available We proposed a method for numerically solving the problem of flow distribution in hydraulic circuits with lumped parameters for the case of random closing relations. The conventional and unconventional types of relations for the laws of isothermal steady fluid flow through the individual hydraulic circuit components are studied. The unconventional relations are presented by those given implicitly by the flow rate and dependent on the pressure of the working fluid. In addition to the unconventional relations, the formal conditions of applicability were introduced. These conditions provide a unique solution to the flow distribution problem. A new modified nodal pressure method is suggested. The method is more versatile in terms of the closing relation form as compared to the unmodified one, and has lower computational costs as compared to the known technique of double-loop iteration. The paper presents an analysis of the new method and its algorithm, gives a calculated example of a gas transportation network, and its results.

  10. Genetically modified yeast of the species Issatchenkia orientalis and closely relates species, and fermentation processes using same

    Science.gov (United States)

    Suominen, Pirkko [Maple Grove, MN; Aristidou, Aristos [Highland Ranch, CO; Pentilla, Merja [Helsinki, FI; Ilmen, Marja [Helsinki, FI; Ruohonen, Laura [Helsinki, FI; Koivuranta, Kari [Vantaa, FI; Roberg-Perez, Kevin [Minneapolis, MN

    2012-01-17

    Cells of the species Issatchenkia orientalis and closely related yeast species are transformed with a vector to introduce an exogenous lactate dehydrogenase gene. The cells produce lactic acid efficiently and are resistant at low pH, high lactate titer conditions.

  11. Whole-Genome Sequences of Two Closely Related Bacteria, Actinomyces sp. Strain Chiba101 and Actinomyces denticolens DSM 20671T

    Science.gov (United States)

    Ishige, Taichiro; Sekigawa, Yuriko; Kobayashi, Tomoko; Torii, Yasushi; Yokoyama, Eiji; Ishiwata, Hiroyuki; Hamada, Moriyuki; Tamura, Tomohiko; Azuma, Ryozo

    2017-01-01

    ABSTRACT Actinomyces sp. strain Chiba101, isolated from an arthritic leg joint of a pig raised in Japan, is a bacterium closely related to Actinomyces denticolens. Here, we deciphered the complete genome sequence of Actinomyces sp. Chiba101 and the high-quality draft genome sequence of A. denticolens DSM 20671T. PMID:28385845

  12. Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions

    Science.gov (United States)

    Zhang, Yan-Cong; Lin, Kui

    2015-01-01

    Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. PMID:26715828

  13. Composition of the essential oils from underground parts of Valeriana officinalis L. s.l. and several closely related taxa

    NARCIS (Netherlands)

    Bos, Rein; Woerdenbag, Herman J.; Hendriks, Henk; Scheffer, Johannes J. C.

    1997-01-01

    The volatile constituents from roots and rhizomes of Valeriana officinalis L. s.l. and of several closely related Valeriana taxa were investigated by GC and GCMS (EI and NICI) analysis. Seeds were obtained from different botanical gardens in Europe, and the plants investigated were grown in an exper

  14. Gender-related inequalities in the division of family work in close relationships: A social psychological perspective

    NARCIS (Netherlands)

    Kluwer, E.S.; Mikula, G.

    2003-01-01

    We offer a social psychological perspective on gender-related inequalities in close relationships and integrate two lines of research that have focused on the intrapersonal perceptions and interpersonal consequences respectively of the gendered division of labour. We start with a brief summary of

  15. Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences

    NARCIS (Netherlands)

    Speksnijder, A.G.C.L.; Kowalchuk, G.A.; Jong, S. de; Kline, E.; Stephen, J.R.; Laanbroek, H.J.

    2001-01-01

    A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a m

  16. Microvariation Artifacts Introduced by PCR and Cloning of Closely Related 16S rRNA Gene Sequences

    NARCIS (Netherlands)

    Speksnijder, A.G.C.L.; Kowalchuk, G.A.; Jong, de S.; Kline, E.; Stephen, J.R.; Laanbroek, H.J.

    2001-01-01

    A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a m

  17. Gender-related inequalities in the division of family work in close relationships: A social psychological perspective

    NARCIS (Netherlands)

    Kluwer, E.S.; Mikula, G.

    2003-01-01

    We offer a social psychological perspective on gender-related inequalities in close relationships and integrate two lines of research that have focused on the intrapersonal perceptions and interpersonal consequences respectively of the gendered division of labour. We start with a brief summary of re

  18. Identifying the Best-Fitting Factor Structure of the Experience of Close Relations

    DEFF Research Database (Denmark)

    Esbjørn, Barbara Hoff; Breinholst, Sonja; Niclasen, Janni

    2015-01-01

    The aim of this study was to enhance the understanding of cultural and sample differences in the assessment of attachment by examining the factor structure of the Experiences in Close Relationships-Revised (ECR-R). The ECR-R is a self-report measure of adult roman- tic attachment dimensions....... The present study used a Danish sample with the purpose of addressing limitations in previous studies, such as the lack of diversity in cultural back- ground, restricted sample characteristics, and poorly fitting structure models. Participants consisted of 253 parents of children between the ages of 7 and 12...

  19. Beauty is in the 'we' of the beholder: greater agreement on facial attractiveness among close relations.

    Science.gov (United States)

    Bronstad, P Matthew; Russell, Richard

    2007-01-01

    Scientific research on facial attractiveness has focused primarily on elucidating universal factors to which all raters respond consistently. However, recent work has shown that there is also substantial disagreement between raters, highlighting the importance of determining how attractiveness preferences vary among different individuals. We conducted a typical attractiveness ratings study, but took the unusual step of recruiting pairs of subjects who were spouses, siblings, or close friends. The agreement between pairs of affiliated friends, siblings, and spouses was significantly greater than between pairs of strangers drawn from the same race and culture, providing evidence that facial-attractiveness preferences are socially organized.

  20. The structurally disordered paramyxovirus nucleocapsid protein tail domain is a regulator of the mRNA transcription gradient

    Science.gov (United States)

    Cox, Robert M.; Krumm, Stefanie A.; Thakkar, Vidhi D.; Sohn, Maximilian; Plemper, Richard K.

    2017-01-01

    The paramyxovirus RNA-dependent RNA-polymerase (RdRp) complex loads onto the nucleocapsid protein (N)–encapsidated viral N:RNA genome for RNA synthesis. Binding of the RdRp of measles virus (MeV), a paramyxovirus archetype, is mediated through interaction with a molecular recognition element (MoRE) located near the end of the carboxyl-terminal Ntail domain. The structurally disordered central Ntail section is thought to add positional flexibility to MoRE, but the functional importance of this Ntail region for RNA polymerization is unclear. To address this question, we dissected functional elements of Ntail by relocating MoRE into the RNA-encapsidating Ncore domain. Linker-scanning mutagenesis identified a microdomain in Ncore that tolerates insertions. MoRE relocated to Ncore supported efficient interaction with N, MoRE-deficient Ntails had a dominant-negative effect on bioactivity that was alleviated by insertion of MoRE into Ncore, and recombinant MeV encoding N with relocated MoRE grew efficiently and remained capable of mRNA editing. MoRE in Ncore also restored viability of a recombinant lacking the disordered central Ntail section, but this recombinant was temperature-sensitive, with reduced RdRp loading efficiency and a flattened transcription gradient. These results demonstrate that virus replication requires high-affinity RdRp binding sites in N:RNA, but productive RdRp binding is independent of positional flexibility of MoRE and cis-acting elements in Ntail. Rather, the disordered central Ntail section independent of the presence of MoRE in Ntail steepens the paramyxovirus transcription gradient by promoting RdRp loading and preventing the formation of nonproductive polycistronic viral mRNAs. Disordered Ntails may have evolved as a regulatory element to adjust paramyxovirus gene expression. PMID:28168220

  1. Premature Activation of the Paramyxovirus Fusion Protein before Target Cell Attachment with Corruption of the Viral Fusion Machinery*

    Science.gov (United States)

    Farzan, Shohreh F.; Palermo, Laura M.; Yokoyama, Christine C.; Orefice, Gianmarco; Fornabaio, Micaela; Sarkar, Aurijit; Kellogg, Glen E.; Greengard, Olga; Porotto, Matteo; Moscona, Anne

    2011-01-01

    Paramyxoviruses, including the childhood pathogen human parainfluenza virus type 3, enter host cells by fusion of the viral and target cell membranes. This fusion results from the concerted action of its two envelope glycoproteins, the hemagglutinin-neuraminidase (HN) and the fusion protein (F). The receptor-bound HN triggers F to undergo conformational changes that render it competent to mediate fusion of the viral and cellular membranes. We proposed that, if the fusion process could be activated prematurely before the virion reaches the target host cell, infection could be prevented. We identified a small molecule that inhibits paramyxovirus entry into target cells and prevents infection. We show here that this compound works by an interaction with HN that results in F-activation prior to receptor binding. The fusion process is thereby prematurely activated, preventing fusion of the viral membrane with target cells and precluding viral entry. This first evidence that activation of a paramyxovirus F can be specifically induced before the virus contacts its target cell suggests a new strategy with broad implications for the design of antiviral agents. PMID:21799008

  2. The Pathogenomic Sequence Analysis of B. cereus and B.thuringiensis Isolates Closely Related to Bacillus anthracis

    Energy Technology Data Exchange (ETDEWEB)

    Han, Cliff S.; Xie, Gary; Challacombe, Jean F.; Altherr, MichaelR.; Smriti, B.; Bruce, David; Campbell, Connie S.; Campbell, Mary L.; Chen, Jin; Chertkov, Olga; Cleland, Cathy; Dimitrijevic-Bussod, M.; Doggett, Norman A.; Fawcett, John J.; Glavina, Tijana; Goodwin, Lynne A.; Hill, Karen K.; Hitchcock, Penny; Jackson, Paul J.; Keim, Paul; Kewalramani, Avinash Ramesh; Longmire, Jon; Lucas, Susan; Malfatti,Stephanie; McMurry, Kim; Meincke, Linda J.; Misra, Monica; Moseman,Bernice L.; Mundt, Mark; Munk, A. Christine; Okinaka, Richard T.; Parson-Quintana, B.; Reilly, Lee P.; Richardson, Paul; Robinson, DonnaL.; Rubin, Eddy; Saunders, Elizabeth; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Ticknor, Lawrence O.; Wills, Patti L.; Gilna, Payl; Brettin, Thomas S.

    2005-08-18

    The sequencing and analysis of two close relatives of Bacillus anthracis are reported. AFLP analysis of over 300 isolates of B.cereus, B. thuringiensis and B. anthracis identified two isolates as being very closely related to B. anthracis. One, a B. cereus, BcE33L, was isolated from a zebra carcass in Nambia; the second, a B. thuringiensis, 97-27, was isolated from a necrotic human wound. The B. cereus appears to be the closest anthracis relative sequenced to date. A core genome of over 3,900 genes was compiled for the Bacillus cereus group, including Banthracis. Comparative analysis of these two genomes with other members of the B. cereus group provides insight into the evolutionary relationships among these organisms. Evidence is presented that differential regulation modulates virulence, rather than simple acquisition of virulence factors. These genome sequences provide insight into the molecular mechanisms contributing to the host range and virulence of this group of organisms.

  3. [Marks on clothing and skin in absolutely and relatively close distance gunshots with fright weapons].

    Science.gov (United States)

    Nadjem, H; Bohnert, M; Schley, K; Pollak, S

    1996-01-01

    Based on an actual case to be examined-the victim had sustained burning and powder tattooing of the abdominal skin--test shots were performed with blank cartridge guns (Mauser and Umarex revolvers, cal. 380) in order to study the changes occurring on textiles in the area of contact and close range shots. As expected, the extent of burning and smoke soiling depended on whether the propellant of the blank cartridges consisted of nitrocellulose (Nc) or black powder. At the same distance the smokeless nitro-powder caused less soot soiling and burning than black powder. Contact or near contact shots produced tear-like tissue damages due to the pressure of the discharged muzzle gases. When black powder cartridges were used, burn holes larger than the caliber were observed; with Nc blank cartridges the thermal effects were most pronounced if textiles made of thermolabile synthetics were shot at.

  4. Shifts in patterns of microhabitat occupation by six closely related species of mosses along a complex altitudinal gradient.

    Science.gov (United States)

    Watson, Maxine A

    1980-01-01

    Changes in patterns of microhabitat occupation were examined for six closely related moss species (family Polytrichaceae) found growing together along a complex altitudinal gradient on the northeast face of Mount Washington, New Hampshire. Little evidence could be found to support the hypothesis that the relative distributions of these six moss species were determined by competitive interactions occurring among them. Instead, the data support the hypothesis that changing patterns in the relative distributions of these six moss species result from differences in microhabitat availability among sites. The moss species appear to behave in an opportunistic manner, occupying a wide array of microhabitats as these microhabitats become available to them.

  5. Molecular characterization of a naturally occurring intraspecific recombinant begomovirus with close relatives widespread in southern Arabia

    KAUST Repository

    Al-Saleh, Mohammed A

    2014-06-02

    in tomato closely resembled those observed in field infected tomato plants, indicating the virus is the causal agent of the leaf curl disease. The symptoms that developed in tomato seedlings closely resembled those observed in field infected tomato plants, indicating that ToLCSDV is the causal agent of the leaf curl disease in Gezira. 2014 Al-Saleh et al.; licensee BioMed Central Ltd.

  6. A new vanilla species from Costa Rica closely related to V. planifolia (Orchidaceae

    Directory of Open Access Journals (Sweden)

    José B. Azofeifa-Bolaños

    2017-02-01

    Full Text Available We describe a new vanilla species growing in sympatry with Vanilla planifolia Jacks. ex Andrews (Orchidaceae in the province of Limón, Caribbean coast of Costa Rica. The morphology of the reproductive and vegetative organs observed on vines cultivated under shade-house, the nuclear (Internal Transcribed Spacer and plastid (matK nucleotide sequences, as well as the contents of aromatic compounds measured in ripe fruits, show that this species is close to but distinct from V. planifolia. The name V. sotoarenasii M.Pignal, Azofeifa-Bolaños & Grisoni sp. nov. is proposed for this new Vanilla species endemic in Costa Rica. It is especially distinguished from V. planifolia by a reduction of about 30% of the size of the fruits and flowers, by a divergence of ITS sequences for at least two species-conserved nucleotides compared to seven other species of the V. planifolia group, and by the presence of anisic compounds and low content of phenolic compounds (including vanillin in the fruits. These results confirmed the extension of the area of distribution of V. planifolia southward to Costa Rica, where a recent speciation process occurred. Because of its particular agronomic and aromatic properties, V. sotoarenasii sp. nov. could represent a valuable biological resource for the vanilla industry.

  7. Adaptation and modification of three CRISPR loci in two closely related cyanobacteria.

    Science.gov (United States)

    Hein, Stephanie; Scholz, Ingeborg; Voß, Björn; Hess, Wolfgang R

    2013-05-01

    An RNA-based screen was performed to reveal a possible evolutionary scenario for the CRISPR-Cas systems in two cyanobacterial model strains. Following the analysis of a draft genome sequence of Synechocystis sp PCC6714, three different CRISPR-Cas systems were characterized that have different degrees of relatedness to another three CRISPR-Cas systems in Synechocystis sp PCC6803. A subtype III-B system was identified that is extremely conserved between both strains. Strong signals in northern hybridizations and the presence of different spacers (but identical repeats) indicated this system to be active, despite the absence of a known endonuclease candidate gene involved in the maturation of its crRNAs in the two strains. The other two systems were found to differ significantly from each other, with different sets of repeat-spacer arrays and different Cas genes. In view of the otherwise very close relatedness of the two analyzed strains, this is suggestive of an unknown mechanism involved in the replacement of CRISPR-Cas cassettes as a whole. Further RNA analyses revealed the accumulation of crRNAs to be impacted by environmental conditions critical for photoautotropic growth. All six systems are associated with a gene for a possible transcriptional repressor. Indeed, we identified one of these genes, sll7009, as encoding a negative regulator specific for the CRISPR1 subtype I-D system in Synechocystis sp PCC6803.

  8. Asexual reproduction in a close relative of Arabidopsis: a genetic investigation of apomixis in Boechera (Brassicaceae).

    Science.gov (United States)

    Schranz, M Eric; Kantama, Laksana; de Jong, Hans; Mitchell-Olds, Thomas

    2006-01-01

    Understanding apomixis (asexual reproduction through seeds) is of great interest to both plant breeders and evolutionary biologists. The genus Boechera is an excellent system for studying apomixis because of its close relationship to Arabidopsis, the occurrence of apomixis at the diploid level, and its potentially simple inheritance by transmission of a heterochromatic (Het) chromosome. Diploid sexual Boechera stricta and diploid apomictic Boechera divaricarpa (carrying a Het chromosome) were crossed. Flow cytometry, karyotype analysis, genomic in situ hybridization, pollen staining and seed-production measurements were used to analyse the parents and resulting F1, F2 and selected F3 and test-cross (TC) generations. The F1 plant was a low-fertility triploid that produced a swarm of aneuploid and polyploid F2 progeny. Two of the F2 plants were fertile near-tetraploids, and analysis of their F3 and TC progeny revealed that they were sexual and genomically stabilized. The apomictic phenotype was not transmitted by genetic crossing as a single dominant locus on the Het chromosome, suggesting a complex genetic control of apomixis that has implications for future genetic and evolutionary analyses in this group.

  9. Embarrassment When Illness Strikes A Close Relative: A World Mental Health Survey Consortium Multi-Site Study

    Science.gov (United States)

    Ahmedani, Brian K.; Kubiak, Sheryl Pimlott; Kessler, Ronald C.; de Graaf, Ron; Alonso, Jordi; Bruffaerts, Ronny; Zarkov, Zahari; Viana, Maria Carmen; Huang, Y.Q.; Hu, Chiyi; Posada-Villa, Jose A.; Lepine, Jean-Pierre; Angermeyer, Matthias C.; de Girolamo, Giovanni; Karam, Aimee N.; Medina-Mora, Maria Elena; Gureje, Oye; Ferry, Finola; Sagar, Rajesh; Anthony, James C.

    2014-01-01

    Background This global study seeks to estimate the degree to which a family member might feel embarrassed when a close relative is suffering from an alcohol, drug, or mental health condition (ADMC) versus a general medical condition (GMC). To date, most studies have considered embarrassment and stigma in society and internalized by the afflicted individual, but have not assessed family embarrassment in a large scale study. Method In 16 sites of the World Mental Health Surveys (WMHS), standardized assessments were completed including items on family embarrassment. Site matching was used to constrain local socially shared determinants of stigma-related feelings, enabling a conditional logistic regression model that estimates the embarrassment close relatives may hold in relation to family members affected by an ADMC, GMC, or both conditions. Results There was a statistically robust association such that subgroups with an ADMC-affected relative were more likely to feel embarrassed as compared to subgroups with a relative affected by a GMC (p<0.001), even with covariate adjustments for age and sex. Conclusions The pattern of evidence from this research is consistent with conceptual models for interventions that target individual- and family-level stigma-related feelings of embarrassment as might be part of the obstacles to effective early intervention and treatment for ADMC conditions. Macro-level interventions are underway, but micro-level interventions also may be required among family members, along with care for each person with an ADMC. PMID:23298443

  10. A dimensionless relative trajectory estimation algorithm for autonomous imaging of a small astronomical body in a close distance flyby

    Science.gov (United States)

    Ariu, Kaito; Inamori, Takaya; Funase, Ryu; Nakasuka, Shinichi

    2016-08-01

    The world's first micro-spacecraft, "Proximate Object Close flYby with Optical Navigation" (PROCYON) has the advanced mission to approach an asteroid in dozen km (a one-order closer imaging distance compared with previous probes). In such a close distance encounter, the estimation of the relative trajectory of the target is necessary to perform autonomous imaging. However, the estimation is difficult owing to rapid changes of the line-of-sight direction of the target body. To overcome this problem, a novel dimensionless or direction only relative trajectory estimation algorithm, which uses a least square method, is proposed. The evaluation function for the least square method coincides with the error property of picture information to enable all of its calculations to be recursive and linear. It is suited for the implementation on the limited on-board computer. Numerical simulation results indicate that the proposed algorithm should enable the one-order closer flyby observation.

  11. Students' perceptions of parent-adolescent closeness and communication about sexuality: relations with sexual knowledge, attitudes, and behaviors.

    Science.gov (United States)

    Somers, C L; Paulson, S E

    2000-10-01

    The main goal of this study was to explore how parent-adolescent closeness and communication about sexuality were associated with three aspects of adolescent sexuality (sexual knowledge, attitudes and behaviors). Participants were 157 boys and girls in grades 9 to 12 from two suburban high schools in the Midwest. Canonical correlation analyses revealed two significant combinations of variables. First, younger age and less maternal and paternal communication were related to less sexual behavior and less sexual knowledge. Second, being younger and female and receiving less maternal communication was related to less sexual knowledge and more conservative attitudes. Contrary to expectation, higher levels of parental closeness in conjunction with parental communication did not have a significant influence on these adolescents' sexuality. Given the importance of both age and parental communication in predicting adolescent's sexuality in this study, implications concerning the timing of communication become evident.

  12. Political market orientation and its commercial cousin: Close family or distant relatives?

    DEFF Research Database (Denmark)

    Ormrod, Robert P.

    2007-01-01

    the differences between the related terms of "market orientation" and "marketing orientation." Further, the article surveys the political market orientation literature and then discusses the perspective that each approach adopts, the extent to which a distinction is made between a "political market orientation...

  13. New criteria for selecting the origin of DNA replication in Wolbachia and closely related bacteria

    DEFF Research Database (Denmark)

    Ioannidis, Panagiotis; Dunning Hotopp, Julie C; Sapountzis, Panagiotis

    2007-01-01

    , the origin of DNA replication (ori) regions were identified in silico for Wolbachia strains and eleven other related bacteria belonging to Ehrlichia, Anaplasma, and Rickettsia genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in C. crescentus. The Wolbachia ori...

  14. Two-component signal transduction in Bacillus cereus and closely related bacteria

    NARCIS (Netherlands)

    Been, de M.W.H.J.

    2009-01-01

    Bacillus cereus is a Gram-positive pathogen that is recognised as an important cause of food-borne disease worldwide. Within the genus Bacillus, B. cereus and its closest relatives form a homogeneous subdivision that has been termed the B. cereus group. This group includes B. anthracis, a pathogen

  15. Gene regulations in HBV-related liver cirrhosis closely correlate with disease severity.

    Science.gov (United States)

    Lee, Seram; Kim, Soyoun

    2007-09-30

    Liver cirrhosis (LC) is defined as comprising diffuse fibrosis and regenerating nodules of the liver. The biochemical and anatomical dysfunction in LC results from both reduced liver cell number and portal vascular derangement. Although several studies have investigated dysregulated genes in cirrhotic nodules, little is known about the genes implicated in the pathophysiologic change of LC or about their relationship with the degree of decompensation. Here, we applied cDNA microarray analysis using 38 HBsAg-positive LC specimens to identify the genes dysregulated in HBV-associated LC and to evaluate their relation to disease severity. Among 1063 known cancer- and apoptosis-related genes, we identified 104 genes that were significantly up- (44) or down- (60) regulated in LC. Interestingly, this subset of 104 genes was characteristically correlated with the degree of decompensation, called the Pugh-Child classification (20 Pugh-Child A, 10 Pugh-Child B, and 8 Pugh-Child C). Patient samples from Pugh-Child C exhibited a distinct pattern of gene expression relative to those of Pugh-Child A and B. Especially in Pugh-Child C, genes encoding hepatic proteins and metabolizing enzymes were significantly down-regulated, while genes encoding various molecules related to cell replication were up-regulated. Our results suggest that subsets of genes in liver cells correspond to the pathophysiologic change of LC according to disease severity and possibly to hepatocarcinogenesis.

  16. Closed-loop surface-related multiple elimination and its application to simultaneous data reconstruction

    NARCIS (Netherlands)

    Lopez Angarita, G.A.; Verschuur, D.J.

    2015-01-01

    Surface-related multiple elimination (SRME) is one of the most commonly used methods for suppressing surface multiples. However, to obtain an accurate surface multiple estimation, dense source and receiver sampling is required. The traditional approach to this problem is performing data interpolatio

  17. Estrus Traits Derived from Activity Measurements are Heritable and Closely Related to Conventional

    DEFF Research Database (Denmark)

    Ismael, Ahmed Ismael Sayed; Kargo, Morten; Fogh, Anders

    This study was aimed at assessing the genetic parameters for fertility-related traits, comparing the interval from calving to first insemination (ICF) to physical activity traits, especially days from calving to first high activity, DFHA. Data from commercial Holstein herds included insemination...

  18. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential

    Directory of Open Access Journals (Sweden)

    Siragusa Gregory R

    2011-06-01

    Full Text Available Abstract Background Because biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context, we sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricultural and human pathogen. Results Phage whole-genome tetra-nucleotide signatures and proteomic tree topologies correlated closely with host phylogeny. Comparisons of our phage genomes to 26 others revealed three shared COGs; of particular interest within this core genome was an endolysin (PF01520, an N-acetylmuramoyl-L-alanine amidase and a holin (PF04531. Comparative analyses of the evolutionary history and genomic context of these common phage proteins revealed two important results: 1 strongly significant host-specific sequence variation within the endolysin, and 2 a protein domain architecture apparently unique to our phage genomes in which the endolysin is located upstream of its associated holin. Endolysin sequences from our phages were one of two very distinct genotypes distinguished by variability within the putative enzymatically-active domain. The shared or core genome was comprised of genes with multiple sequence types belonging to five pfam families, and genes belonging to 12 pfam families, including the holin genes, which were nearly identical. Conclusions Significant genomic diversity exists even among closely-related bacteriophages. Holins and endolysins represent conserved functions across divergent phage genomes and, as we demonstrate here, endolysins can have significant variability and host-specificity even among closely-related genomes. Endolysins in our phage genomes may be subject to different selective pressures than the rest of the genome. These findings may have important implications for potential biotechnological applications of phage gene products.

  19. Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations

    Directory of Open Access Journals (Sweden)

    Yang Hsin-Chou

    2012-07-01

    Full Text Available Abstract Background Ancestry informative markers (AIMs are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genetics, forensic sciences, and medical genetics. Single nucleotide polymorphisms (SNPs, the materials of AIMs, are useful for classifying individuals from distinct continental origins but cannot discriminate individuals with subtle genetic differences from closely related ancestral lineages. Proof-of-principle studies have shown that gene expression (GE also is a heritable human variation that exhibits differential intensity distributions among ethnic groups. GE supplies ethnic information supplemental to SNPs; this motivated us to integrate SNP and GE markers to construct AIM panels with a reduced number of required markers and provide high accuracy in ancestry inference. Few studies in the literature have considered GE in this aspect, and none have integrated SNP and GE markers to aid classification of samples from closely related ethnic populations. Results We integrated a forward variable selection procedure into flexible discriminant analysis to identify key SNP and/or GE markers with the highest cross-validation prediction accuracy. By analyzing genome-wide SNP and/or GE markers in 210 independent samples from four ethnic groups in the HapMap II Project, we found that average testing accuracies for a majority of classification analyses were quite high, except for SNP-only analyses that were performed to discern study samples containing individuals from two close Asian populations. The average testing accuracies ranged from 0.53 to 0.79 for SNP-only analyses and increased to around 0.90 when GE markers were integrated together with SNP markers for the classification of samples from closely related Asian populations. Compared to GE-only analyses, integrative analyses of SNP and GE markers showed comparable testing

  20. The evolution of different maternal investment strategies in two closely related desert vertebrates

    Science.gov (United States)

    Ennen, Joshua R.; Lovich, Jeffrey E.; Averill-Murray, Roy C.; Yackulic, Charles B.; Agha, Mickey; Loughran, Caleb; Tennant, Laura A.; Sinervo, Barry

    2017-01-01

    We compared egg size phenotypes and tested several predictions from the optimal egg size (OES) and bet-hedging theories in two North American desert-dwelling sister tortoise taxa, Gopherus agassizii and G. morafkai, that inhabit different climate spaces: relatively unpredictable and more predictable climate spaces, respectively. Observed patterns in both species differed from the predictions of OES in several ways. Mean egg size increased with maternal body size in both species. Mean egg size was inversely related to clutch order in G. agassizii, a strategy more consistent with the within-generation hypothesis arising out of bet-hedging theory or a constraint in egg investment due to resource availability, and contrary to theories of density dependence, which posit that increasing hatchling competition from later season clutches should drive selection for larger eggs. We provide empirical evidence that one species, G. agassizii, employs a bet-hedging strategy that is a combination of two different bet-hedging hypotheses. Additionally, we found some evidence for G. morafkai employing a conservative bet-hedging strategy. (e.g., lack of intra- and interclutch variation in egg size relative to body size). Our novel adaptive hypothesis suggests the possibility that natural selection favors smaller offspring in late-season clutches because they experience a more benign environment or less energetically challenging environmental conditions (i.e., winter) than early clutch progeny, that emerge under harsher and more energetically challenging environmental conditions (i.e., summer). We also discuss alternative hypotheses of sexually antagonistic selection, which arise from the trade-offs of son versus daughter production that might have different optima depending on clutch order and variation in temperature-dependent sex determination (TSD) among clutches. Resolution of these hypotheses will require long-term data on fitness of sons versus daughters as a function of

  1. Ethical Challenges when Interviewing Close Relatives Together – An Integrative Review

    DEFF Research Database (Denmark)

    Voltelen, Barbara; Konradsen, Hanne; Østergaard, Birte

    2015-01-01

    . The purpose of this study is to describe the special ethical perspectives concerning joint interviews with interrelated persons. Method An integrative review was performed. A search was conducted in Pub Med, Cinahl, Philosophers Index and Academic Search from 1980 -2014. Data corpus from the 17 articles...... was analysed using thematic analysis with an inductive approach searching for themes about ethical considerations doing joint interviews. The SPIDER search tool was applied using keywords relatives, ethic, dyadic interview, challenges and qualitative methods created on the basis of relevant pseudonyms, Mesh...

  2. Solvent-Induced Reversal of Activities between Two Closely Related Heterogeneous Catalysts in the Aldol Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Kandel, Kapil [Ames Laboratory; Althaus, Stacey M [Ames Laboratory; Peeraphatdit, Chorthip [Ames Laboratory; Kobayashi, Takeshi [Ames Laboratory; Trewyn, Brian G [Ames Laboratory; Pruski, Marek [Ames Laboratory; Slowing, Igor I [Ames Laboratory

    2013-01-11

    The relative rates of the aldol reaction catalyzed by supported primary and secondary amines can be inverted by 2 orders of magnitude, depending on the use of hexane or water as a solvent. Our analyses suggest that this dramatic shift in the catalytic behavior of the supported amines does not involve differences in reaction mechanism, but is caused by activation of imine to enamine equilibria and stabilization of iminium species. The effects of solvent polarity and acidity were found to be important to the performance of the catalytic reaction. This study highlights the critical role of solvent in multicomponent heterogeneous catalytic processes.

  3. Dispersal and Transmission of Avian Paramyxovirus Serotype 4 among Wild Birds and Domestic Poultry

    Directory of Open Access Journals (Sweden)

    Renfu Yin

    2017-05-01

    Full Text Available Avian paramyxovirus serotype 4 (APMV-4 is found sporadically in wild birds worldwide, and it is an economically important poultry pathogen. Despite the existence of several published strains, very little is known about the distribution, host species, and transmission of APMV-4 strains. To better understand the relationships among these factors, we conducted an APMV-4 surveillance of wild birds and domestic poultry in six provinces of China suspected of being intercontinental flyways and sites of interspecies transmission. APMV-4 surveillance was conducted in 9,160 wild birds representing seven species, and 1,461 domestic poultry in live bird markets (LMBs from December 2013 to June 2016. The rate of APMV-4 isolation was 0.10% (11/10,621, and viruses were isolated from swan geese, bean geese, cormorants, mallards, and chickens. Sequencing and phylogenetic analyses of the 11 isolated viruses indicated that all the isolates belonging to genotype I were epidemiologically connected with wild bird-origin viruses from the Ukraine and Italy. Moreover, chicken-origin APMV-4 strains isolated from the LBMs were highly similar to wild bird-origin viruses from nearby lakes with free-living wild birds. In additional, a hemagglutination-negative APMV-4 virus was identified. These findings, together with recent APMV-4 studies, suggest potential virus interspecies transmission between wild birds and domestic poultry, and reveal possible epidemiological intercontinental connections between APMV-4 transmission by wild birds.

  4. Characterization of avian paramyxovirus type 1 from migratory wild birds in chickens.

    Science.gov (United States)

    Shim, Jong-Bo; So, Hyun-Hee; Won, Ho-Keun; Mo, In-Pil

    2011-12-01

    Newcastle disease virus (NDV) is one of the most important infectious agents in the poultry industry, and vaccines against it have been widely used for prevention and control. Live vaccines, which can replicate in the respiratory and digestive systems, have been especially needed in areas with outbreaks of viscerotropic velogenic Newcastle disease. Towards the goal of searching for a new live vaccine candidate, avian paramyxovirus type 1 (APMV-1) was isolated from the faeces of wild birds. Three APMV-1 strains thus isolated were characterized in terms of phylogeny, pathogenicity, immunogenicity and tissue tropism, and on the basis of these analyses were classified as lentogenic genotype I NDV. CBU2179, one of the three APMV-1 strains, was selected and was evaluated in terms of its efficacy and safety in specific pathogen-free chickens and commercial broilers. The manufactured trial vaccine from this strain, also called CBU2179, induced similar immune responses to those of VG/GA and B1 commercial vaccines, and provided 100% protection against challenge from viscerotropic velogenic NDV, KJW/49 strain (the official challenge strain in Korea). Also, the CBU2179 virus was re-isolated and persisted as long as or longer than other vaccine strains in both the respiratory and alimentary tracts. Therefore, the CBU2179 strain may represent a good candidate for a live Newcastle disease vaccine to protect chickens against viscerotropic velogenic NDV.

  5. Altered Function in CD8+ T Cells following Paramyxovirus Infection of the Respiratory Tract

    Science.gov (United States)

    Gray, Peter M.; Arimilli, Subhashini; Palmer, Ellen M.; Parks, Griffith D.; Alexander-Miller, Martha A.

    2005-01-01

    For many respiratory pathogens, CD8+ T cells have been shown to play a critical role in clearance. However, there are still many unanswered questions with regard to the factors that promote the most efficacious immune response and the potential for immunoregulation of effector cells at the local site of infection. We have used infection of the respiratory tract with the model paramyxovirus simian virus 5 (SV5) to study CD8+ T-cell responses in the lung. For the present study, we report that over time a population of nonresponsive, virus-specific CD8+ T cells emerged in the lung, culminating in a lack of function in ∼85% of cells specific for the immunodominant epitope from the viral matrix (M) protein by day 40 postinfection. Concurrent with the induction of nonresponsiveness, virus-specific cells that retained function at later times postinfection exhibited an increased requirement for CD8 engagement. This change was coupled with a nearly complete loss of functional phosphoprotein-specific cells, a response previously shown to be almost exclusively CD8 independent. These studies add to the growing evidence for immune dysregulation following viral infection of the respiratory tract. PMID:15731228

  6. Status of wild birds in Bulgarian zoos with regard to orthomyxovirus and paramyxovirus type 1 infections.

    Science.gov (United States)

    Dimitrov, Kiril M; Manvell, Ruth J; Goujgoulova, Gabriela V

    2010-03-01

    Newcastle disease virus (NDV) and avian influenza virus (AIV) are pathogens of major economic and social importance, and the diseases they cause are often devastating, particularly in domestic poultry. Both viruses are naturally found in a wide variety of wild birds, particularly aquatic species, where asymptomatic infection typically occurs. Wild birds are therefore considered to be a natural reservoir for both viruses. Wild birds kept in captivity are in an environment that promotes transmission of infection with both influenza and Newcastle disease viruses. This report describes a survey for the detection of antibodies against Newcastle disease and avian influenza A viruses using the hemagglutination inhibition test in samples from 88 wild birds from 38 species in four Bulgarian zoos. Samples with positive results against NDV were also tested against avian paramyxovirus type 3 (APMV-3). Real-time reverse-transcriptase PCR was also performed to detect viral RNA of NDV and AIV among 127 wild birds from 57 species from the same zoos. In 13 samples from seven avian species (ten birds from the family Phasianidae, two from the family Numidae, and one from the family Columbidae), antibodies against APMV-1 were detected. Seven birds, whose sera were APMV-1 positive, had been vaccinated. The other six birds (five Phasianidae representatives and one of the Columbidae family) had no immunization history. No antibodies against both H5 and H7 AIV and against APMV-3 were detected, and no RNA of NDV and AIV were detected.

  7. SEROLOGICAL EVIDENCE OF AVIAN PARAMYXOVIRUS-2 INFECTION IN BACKYARD AND COMMERCIAL POULTRY BIRDS IN SAUDI ARABIA

    Directory of Open Access Journals (Sweden)

    A. N. ALKHALAF

    2009-07-01

    Full Text Available Serological survey was conducted to detect avian paramyxovirus serotype-2 (APMV-2 antibodies in commercial and backyard bird flocks, using Enzyme-linked immunosorbent assay (ELISA and haemagglutination inhibition (HI test. Sera were collected from 212 commercial and 56 backyard birds. Age of commercial birds ranged from one-day old to 62 weeks. In the backyard birds, seroprevalence of APVM-2 was 71.42 and 78.57%, whereas this seroprevalence was 52.35 and 60.84% using the HI test and the ELISA, respectively in commercial poultry birds. No antibodies against APMV-2 were detected in 1-5 days old chicks with either test. The HI test showed the highest positive samples (P<0.05 of APMV-2 in 19-35 days age group (58.33%, followed by age group 11-18 weeks (51.35% and 25-62 weeks (47.05%. Similarly, ELISA also showed the highest positive samples of APMV-2 (68.75% in 19-35 days age group (P<0.05, followed by age group 11-18 weeks (62.16% and 25-62 weeks (56.86%. In conclusion, this study indicated the presence of antibodies to APMV-2 among backyard and commercial poultry birds in Saudi Arabia.

  8. Ethical Challenges when Interviewing Close Relatives Together – An Integrative Review

    DEFF Research Database (Denmark)

    Voltelen, Barbara; Konradsen, Hanne; Østergaard, Birte

    2015-01-01

    Background and purpose Interviewing two interrelated persons (or more) simultaneously might pose different ethical considerations than interviewing just one person. Such ethical considerations, however, remain largely undescribed in literature, challenging the researcher who wishes to conduct them...... was analysed using thematic analysis with an inductive approach searching for themes about ethical considerations doing joint interviews. The SPIDER search tool was applied using keywords relatives, ethic, dyadic interview, challenges and qualitative methods created on the basis of relevant pseudonyms, Mesh......: The researcher/interviewer, Planning of joint interviews and Participant well-being. Conclusions and implications The nature of joint interviews poses many ethical challenges as more people are involved. They provide insight into shared accounts and communication patterns between interviewees, highlighting...

  9. Estrus Traits Derived from Activity Measurements are Heritable and Closely Related to Conventional

    DEFF Research Database (Denmark)

    Ismael, Ahmed Ismael Sayed; Kargo, Morten; Fogh, Anders

    This study was aimed at assessing the genetic parameters for fertility-related traits, comparing the interval from calving to first insemination (ICF) to physical activity traits, especially days from calving to first high activity, DFHA. Data from commercial Holstein herds included insemination...... dates of 11,363 cows for ICF. The activity traits were derived from electronic activity tags for 3533 Holstein cows. Estimates of heritability were 0.05 for ICF and 0.15 for DFHA. The genetic correlation between ICF and DFHA was strong (0.92). The high heritability estimate and the strong genetic...... correlation between ICF and DFHA suggest that genetic gain in ICF can be improved by including DFHA as a supplementary trait in the genetic evaluation of female fertility...

  10. Genetic rescue of an endangered domestic animal through outcrossing with closely related breeds

    DEFF Research Database (Denmark)

    Strønen, Astrid Vik; Salmela, Elina; Baldursdottir, Birna K.

    2017-01-01

    Genetic rescue, outcrossing with individuals from a related population, is used to augment genetic diversity in populations threatened by severe inbreeding and extinction. The endangered Norwegian Lundehund dog underwent at least two severe bottlenecks in the 1940s and 1960s that each left only......: Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48 dogs from the four breeds revealed substantially lower genetic diversity for the Lundehund (HE 0.035) than for other breeds (HE 0.209-0.284). Analyses of genetic...... structure with > 15K linkage disequilibrium-pruned SNPs showed four distinct genetic clusters. Pairwise FST values between Lundehund and the candidate breeds were highest for Icelandic Sheepdog, followed by Buhund and Norrbottenspets. We assessed the presence of outlier loci among candidate breeds...

  11. Plant Virus Differentially Alters the Plant's Defense Response to Its Closely Related Vectors

    Science.gov (United States)

    Shi, Xiaobin; Pan, Huipeng; Xie, Wen; Wu, Qingjun; Wang, Shaoli; Liu, Yang; Fang, Yong; Chen, Gong; Gao, Xiwu; Zhang, Youjun

    2013-01-01

    Background The whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), is one of the most widely distributed agricultural pests. In recent years, B. tabaci Q has invaded China, and Q has displaced B in many areas now. In a number of regions of the world, invasion by B and/or Q has been followed by outbreaks of tomato yellow leaf curl virus (TYLCV). Our previous study showed TYLCV directly and indirectly modified the feeding behavior of B. tabaci in favor of Q rather than B. Methodology/Principal Findings In this study, we quantified the salicylic acid (SA) titers and relative gene expression of SA in tomato leaves that were infested with viruliferous or non-viruliferous B and Q. We also measured the impacts of exogenous SA on the performance of B and Q, including the effects on ovary development. SA titer was always higher in leaves that were infested with viruliferous B than with viruliferous Q, whereas the SA titer did not differ between leaves infested with non-viruliferous B and Q. The relative gene expression of SA signaling was increased by feeding of viruliferous B but was not increased by feeding of viruliferous Q. The life history traits of B and Q were adversely affected on SA-treated plants. On SA-treated plants, both B and Q had lower fecundity, shorter longevity, longer developmental time and lower survival rate than on untreated plants. Compared with whiteflies feeding on control plants, those feeding on SA-treated plants had fewer oocytes and slower ovary development. On SA-treated plants, viruliferous B had fewer oocytes than viruliferous Q. Conclusions/Significance These results indicate that TYLCV tends to induce SA-regulated plant defense against B but SA-regulated plant defense against Q was reduced. In other words, Q may have a mutualistic relationship with TYLCV that results in the reduction of the plant's defense response. PMID:24391779

  12. Characterisation data of simple sequence repeats of phages closely related to T7M

    Directory of Open Access Journals (Sweden)

    Tiao-Yin Lin

    2016-09-01

    Full Text Available Coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2 share high homology in genomic sequences. Simple sequence repeats (SSRs are found in their genomes and variations of SSRs among these phages are observed. Analyses on regions of sequences in T7M and T3 genomes that are likely derived from phage recombination, as well as the counterparts in ϕYeO3-12 and ϕSG-JL2, have been discussed by Lin in “Simple sequence repeat variations expedite phage divergence: mechanisms of indels and gene mutations” [1]. These regions are referred to as recombinant regions. The focus here is on SSRs in the whole genome and regions of sequences outside the recombinant regions, referred to as non-recombinant regions. This article provides SSR counts, relative abundance, relative density, and GC contents in the complete genome and non-recombinant regions of these phages. SSR period sizes and motifs in the non-recombinant regions of phage genomes are plotted. Genomic sequence changes between T7M and T3 due to insertions, deletions, and substitutions are also illustrated. SSRs and nearby sequences of T7M in the non-recombinant regions are compared to the sequences of ϕYeO3-12 and ϕSG-JL2 in the corresponding positions. The sequence variations of SSRs due to vertical evolution are classified into four categories and tabulated: (1 insertion/deletion of SSR units, (2 expansion/contraction of SSRs without alteration of genome length, (3 changes of repeat motifs, and (4 generation/loss of repeats.

  13. Different mechanics of snap-trapping in the two closely related carnivorous plants Dionaea muscipula and Aldrovanda vesiculosa

    CERN Document Server

    Poppinga, Simon

    2011-01-01

    The carnivorous aquatic Waterwheel Plant (Aldrovanda vesiculosa L.) and the closely related terrestrial Venus Flytrap (Dionaea muscipula SOL. EX J. ELLIS) both feature elaborate snap-traps, which shut after reception of an external mechanical stimulus by prey animals. Traditionally, Aldrovanda is considered as a miniature, aquatic Dionaea, an assumption which was already established by Charles Darwin. However, videos of snapping traps from both species suggest completely different closure mechanisms. Indeed, the well-described snapping mechanism in Dionaea comprises abrupt curvature inversion of the two trap lobes, while the closing movement in Aldrovanda involves deformation of the trap midrib but not of the lobes, which do not change curvature. In this paper, we present the first detailed mechanical models for these plants, which are based on the theory of thin solid membranes and explain this difference by showing that the fast snapping of Aldrovanda is due to kinematic amplification of the bending deforma...

  14. Domestication and defence: Foliar tannins and C/N ratios in cassava and a close wild relative

    Science.gov (United States)

    Mondolot, Laurence; Marlas, Amandine; Barbeau, Damien; Gargadennec, Annick; Pujol, Benoît; McKey, Doyle

    2008-09-01

    Plant domestication is accompanied by shifts in resource allocation, as a result of farmer selection for genotypes that give high yields in agricultural habitats. Relaxed natural selection for chemical and physical defences in these habitats could facilitate resource allocation to yield. We compared the concentrations of tannins, and C/N ratios, which are often correlated with investment in cell-wall compounds, in leaves of landraces of domesticated cassava ( Manihot esculenta) and a close wild relative in French Guiana. Foliar concentrations of tannins were about 1.9 times higher in the wild relative than in domesticated cassava. Histochemical analyses showed that tannins were present in nearly all palisade and spongy parenchyma cells of the wild taxon, but in only some cells of these tissues in M. esculenta. C/N ratios were also 1.9 times higher in leaves of the wild relative than in those of domesticated cassava. Tannins accounted for only a small proportion of total carbon, and the higher C/N ratio in wild than in domesticated cassava may reflect higher investment in carbon-containing compounds additional to tannins, such as cell-wall compounds. The divergence in these traits between cassava and this close wild relative mirrors a broad pattern observed in wild plant species across habitats varying in resource availability. One explanation for our results is that domestication in cassava may have favoured a shift from a resource conservation strategy to a resource acquisition strategy.

  15. RUGBY GAME-RELATED STATISTICS THAT DISCRIMINATE BETWEEN WINNING AND LOSING TEAMS IN IRB AND SUPER TWELVE CLOSE GAMES

    Directory of Open Access Journals (Sweden)

    Luis Vaz

    2010-03-01

    Full Text Available The aim of the current study was to identify the Rugby game- related statistics that discriminated between winning and losing teams in IRB and S12 close games. Archival data reported to game-related statistics from 120 IRB games and 204 Super Twelve games played between 2003 and 2006. Afterwards, a cluster analysis was conducted to establish, according to game final score differences, three different match groups. Only the close games group was selected for further analysis (IRB n = 64 under 15 points difference and Super Twelve n = 95 under 11 points difference. An analysis to the structure coefficients (SC obtained through a discriminant analysis allowed to identify the most powerful game-related statistics in discriminating between winning and losing teams. The discriminant functions were statistically significant for Super Twelve games (Chi-square = 33.8, p < 0.01, but not for IRB games (Chi- square = 9.4, p = n.s.. In the first case, winners and losers were discriminated by possessions kicked (SC = 0.48, tackles made (SC = 0.45, rucks and pass (SC = -0.40, passes completed (SC = 0. 39, mauls won (SC = -0.36, turnovers won (SC = -0.33, kicks to touch (SC = 0.32 and errors made (SC = -0.32. The minus sign denotes higher values in losing teams. Rugby game-related statistics were able to discriminate between winners and losers in Super Twelve close games and suggest that a kicking based game supported by an effective defensive structure is more likely to win matches than a possession based one

  16. Transposons play an important role in the evolution and diversification of centromeres among closely related species

    Directory of Open Access Journals (Sweden)

    Scott eJackson

    2015-04-01

    Full Text Available Centromeres are important chromosomal regions necessary for eukaryotic cell segregation and replication. Due to high amounts of tandem repeats and transposons, centromeres have been difficult to sequence in most multicellular organisms, thus their sequence structure and evolution are poorly understood. In this study, we analyzed transposons in the centromere 8 (Cen8 from the African cultivated rice (O. glaberrima and two subspecies of the Asian cultivated rice (O. sativa, indica and japonica. We detected much higher transposon contents (>69% in centromere regions than in the whole genomes of O. sativa ssp japonica and O. glaberrima (~35%. We compared the three Cen8s and identified numerous recent insertions of transposons that were frequently organized into multiple-layer nested blocks, similar to nested transposons in maize. Except for the Hopi retrotransposon, all LTR retrotransposons were shared but exhibit different abundances amongst the three Cen8s. Even though a majority of the transposons were located in intergenic regions, some gene-related transposons were found and may be involved in gene diversification. Chromatin immunoprecipitated (ChIP data analysis revealed that 165 families from both Class I and Class II transposons were found in CENH3-associated chromatin sequences. These results indicate essential roles for transposons in centromeres and that the rapid divergence of the Cen8 sequences between the two cultivated rice species was primarily caused by recent transposon insertions.

  17. Locomotor performance of closely related Tropidurus species: relationships with physiological parameters and ecological divergence.

    Science.gov (United States)

    Kohlsdorf, Tiana; James, Rob S; Carvalho, José E; Wilson, Robbie S; Dal Pai-Silva, Maeli; Navas, Carlos A

    2004-03-01

    Tropidurid lizards have colonized a variety of Brazilian open environments without remarkable morphological variation, despite ecological and structural differences among habitats used. This study focuses on two Tropidurus sister-species that, despite systematic proximity and similar morphology, exhibit great ecological divergence and a third ecologically generalist congeneric species providing an outgroup comparison. We quantified jumping capacity and sprint speed of each species on sand and rock to test whether ecological divergence was also accompanied by differences in locomotor performance. Relevant physiological traits possibly associated with locomotor performance - metabolic scopes and fiber type composition, power output and activity of the enzymes citrate synthase, pyruvate kinase and lactate dehydrogenase of the iliofibularis muscle - were also compared among the three Tropidurus species. We found that the two sister-species exhibited remarkable differences in jumping performance, while Tropidurus oreadicus, the more distantly related species, exhibited intermediate values. Tropidurus psamonastes, a species endemic to sand dunes, exhibited high absolute sprint speeds on sand, jumped rarely and possessed a high proportion of glycolytic fibers and low activity of citrate synthase. The sister-species Tropidurus itambere, endemic to rocky outcrops, performed a large number of jumps and achieved lower absolute sprint speed than T. psamonastes. This study provides evidence of rapid divergence of locomotor parameters between sister-species that use different substrates, which is only partially explained by variation in physiological parameters of the iliofibularis muscle.

  18. Rediscovery of Trypanosoma (Pycnomonas) suis, a tsetse-transmitted trypanosome closely related to T. brucei.

    Science.gov (United States)

    Hutchinson, Rachel; Gibson, Wendy

    2015-12-01

    The African tsetse-transmitted trypanosomes are considered to be a well-known group of parasitic protozoa, but in 2008 a novel and distinctive trypanosome related to Trypanosoma brucei was discovered among tsetse isolates from Msubugwe in Tanzania. The host range, distribution and potential pathogenicity of this new trypanosome remain to be elucidated; such studies would be facilitated by a sensitive and specific identification method. Here, we identified two highly repetitive elements in the genome of the new trypanosome: a 177 bp repeat, which was located predominantly on the highly abundant minichromosomes, and a 138 bp repeat, which was widely dispersed in the genome. A PCR test based on each repeat was specific for the new trypanosome and sensitive to Trypanosoma (Pycnomonas) suis. We also present data on the molecular karyotype and spliced leader (SL, miniexon) repeat of the new trypanosome, both of which distinguish T. suis from other, better-known African tsetse-transmitted trypanosomes. The rediscovery of T. suis opens new lines of research into the evolution and biology of the African trypanosomes.

  19. Closely related intertidal and deep-sea Halomonhystera species have distinct fatty acid compositions

    Science.gov (United States)

    Van Campenhout, Jelle; Vanreusel, Ann

    2017-01-01

    The deep-sea free-living nematode Halomonhystera hermesi, dominant in the sulphidic sediments of the Håkon Mosby mud volcano (1280 m, Barent sea slope), is part of the mainly estuarine Halomonhystera disjuncta species complex consisting of five cryptic species (GD1-GD5). Cryptic species have a very similar morphology raising questions on their specific environmental differences. This study analyzed total fatty acid (FA) compositions of H. hermesi and GD1, one of H. hermesi's closest relatives. Additionally, we experimentally investigated the effect of a temperature reduction, salinity increase and sulphide concentrations on GD1's FA composition. Because nematodes are expected to have low amounts of storage FA, total FA compositions most likely reflect FA contents of cellular membranes. The deep-sea nematode H. hermesi had significantly lower saturation levels and increased highly unsaturated fatty acid (HUFAs) proportions due to the presence of docosahexanoic acid (DHA—22:6ω3) and higher eicosapentaenoic acid (EPA—20:5ω3) proportions. HUFAs were absent in H. hermesi's food source indicating the ability and need for this nematode to synthesize HUFAs in a deep-sea environment. Our experimental data revealed that only a decrease in temperature resulted in lower saturated fatty acids proportions, indicating that the FA content of H. hermesi is most likely a response to temperature but not to sulphide concentrations or salinity differences. In experimental nematodes, EPA proportions were low and DHA was absent indicating that other factors than temperature, salinity and sulphides mediate the presence of these HUFAs in H. hermesi.

  20. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus in China with multiple gene markers.

    Directory of Open Access Journals (Sweden)

    Qing-Yan Dai

    Full Text Available Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI gene and two alternative internal transcribed spacer (ITS genes (ITS1 and ITS2. Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML/Neighbor-joining (NJ, "best close match" (BCM, Minimum distance (MD, and BP-based method (BP, representing commonly used methodology (tree-based and non-tree based in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In

  1. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

    Science.gov (United States)

    Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

    2012-01-01

    Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our

  2. Transcriptomic Analyses Elucidate Adaptive Differences of Closely Related Strains of Pseudomonas aeruginosa in Fuel

    Energy Technology Data Exchange (ETDEWEB)

    Gunasekera, Thusitha S.; Bowen, Loryn L.; Zhou, Carol E.; Howard-Byerly, Susan C.; Foley, William S.; Striebich, Richard C.; Dugan, Larry C.; Ruiz, Oscar N.; Stams, Alfons J. M.

    2017-03-17

    Pseudomonas aeruginosacan utilize hydrocarbons, but different strains have various degrees of adaptation despite their highly conserved genome.P. aeruginosaATCC 33988 is highly adapted to hydrocarbons, whileP. aeruginosastrain PAO1, a human pathogen, is less adapted and degrades jet fuel at a lower rate than does ATCC 33988. We investigated fuel-specific transcriptomic differences between these strains in order to ascertain the underlying mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat shock response, membrane proteins, efflux pumps, and several novel genes were upregulated in ATCC 33988. Overexpression ofalkgenes in PAO1 provided some improvement in growth, but it was not as robust as that of ATCC 33988, suggesting the role of other genes in adaptation. Expression of the function unknown gene PA5359 from ATCC 33988 in PAO1 increased the growth in fuel. Bioinformatic analysis revealed that PA5359 is a predicted lipoprotein with a conserved Yx(FWY)xxD motif, which is shared among bacterial adhesins. Overexpression of the putative resistance-nodulation-division (RND) efflux pump PA3521 to PA3523 increased the growth of the ATCC 33988 strain, suggesting a possible role in fuel tolerance. Interestingly, the PAO1 strain cannot utilizen-C8andn-C10. The expression of green fluorescent protein (GFP) under the control ofalkBpromoters confirmed thatalkgene promoter polymorphism affects the expression ofalkgenes. Promoter fusion assays further confirmed that the regulation ofalkgenes was different in the two strains. Protein sequence analysis

  3. Transcriptomic Analyses Elucidate Adaptive Differences of Closely-Related Strains of P. aeruginosa in Fuel.

    Science.gov (United States)

    Gunasekera, Thusitha S; Bowen, Loryn L; Zhou, Carol E; Howard-Byerly, Susan C; Foley, William S; Striebich, Richard C; Dugan, Larry C; Ruiz, Oscar N

    2017-03-17

    Pseudomonas aeruginosa can utilize hydrocarbons, but different strains have varying degrees of adaptation despite their highly conserved genome. P. aeruginosa ATCC 33988 is highly adapted to hydrocarbons while strain PAO1, a human pathogen, is less-adapted and degrades jet fuel at a slower rate than does ATCC 33988. We investigated fuel specific transcriptomic differences between these strains in order to ascertain the underling mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat-shock response, membrane proteins, efflux pumps and several novel genes were upregulated in ATCC 33988. Overexpression of alk genes in PAO1 provided some improvement in growth, but not as robust as that of ATCC 33988, suggesting the role of other genes in adaptation. Expression of the function unknown gene PA5359 from ATCC 33988 in PAO1 increased the growth in fuel. Bioinformatic analysis revealed that PA5359 is a predicted lipoprotein with a conserved 'Yx(FWY)xxD' motif, which is shared among bacterial adhesins. Overexpression of the putative RND-efflux pump PA3521-PA3523 increased the growth of ATCC 33988 strain suggesting a possible role in fuel tolerance. Interestingly the PAO1 strain cannot utilize nC8 and nC10. Expression of GFP under the control of alkB promoters confirmed that alk gene promoter polymorphism affects the expression of alk genes. Promoter fusion assays further confirmed that regulation of alk genes was different in the two strains. Protein sequence analysis showed low amino acid differences for many of the upregulated genes, further supporting transcriptional control as the main mechanism for enhanced adaptation.IMPORTANCE These results support that specific signal transduction, gene regulation and coordination of multiple biological responses are required to improve survival, growth and metabolism of fuel in adapted strains. This study provides new insight into the mechanistic

  4. High pathogenicity and low genetic evolution of avian paramyxovirus type I (Newcastle disease virus) isolated from live bird markets in Uganda.

    Science.gov (United States)

    Byarugaba, Denis K; Mugimba, Kizito K; Omony, John B; Okitwi, Martin; Wanyana, Agnes; Otim, Maxwell O; Kirunda, Halid; Nakavuma, Jessica L; Teillaud, Angélique; Paul, Mathilde C; Ducatez, Mariette F

    2014-10-01

    Newcastle disease is still a serious disease of poultry especially in backyard free-range production systems despite the availability of cross protective vaccines. Healthy-looking poultry from live bird markets have been suspected as a major source of disease spread although limited studies have been conducted to ascertain the presence of the virulent strains in the markets and to understand how they are related to outbreak strains. This study evaluated the occurrence of Newcastle disease virus in samples collected from poultry in live bird markets across Uganda. The isolates were pathoyped using standard methods (mean death time (MDT), intracelebral pathogenicity index (ICPI), and sequencing of the fusion protein cleavage site motif) and also phylogenetically analysed after sequencing of the full fusion and hemagglutin-neuraminidase genes. The isolates were classified into genotypes and subgenotypes based on the full fusion protein gene classification system and compared with other strains in the region and world-wide. Virulent avian paramyxovirus type I (APMV-1) (Newcastle disease virus) was isolated in healthy-looking poultry in live bird markets. The viruses belonged to a new subgenotype, Vd, in genotype V, and clustered together with Tanzania and Kenya strains. They harbored low genetic diversity. The occurrence of virulent AMPV-1 strains in live bird markets may serve as sources of Newcastle disease outbreaks in non-commercial farms.

  5. A family-wide RT-PCR assay for detection of paramyxoviruses and application to a large-scale surveillance study.

    Directory of Open Access Journals (Sweden)

    Sander van Boheemen

    Full Text Available Family-wide molecular diagnostic assays are valuable tools for initial identification of viruses during outbreaks and to limit costs of surveillance studies. Recent discoveries of paramyxoviruses have called for such assay that is able to detect all known and unknown paramyxoviruses in one round of PCR amplification. We have developed a RT-PCR assay consisting of a single degenerate primer set, able to detect all members of the Paramyxoviridae family including all virus genera within the subfamilies Paramyxovirinae and Pneumovirinae. Primers anneal to domain III of the polymerase gene, with the 3' end of the reverse primer annealing to the conserved motif GDNQ, which is proposed to be the active site for nucleotide polymerization. The assay was fully optimized and was shown to indeed detect all available paramyxoviruses tested. Clinical specimens from hospitalized patients that tested positive for known paramyxoviruses in conventional assays were also detected with the novel family-wide test. A high-throughput fluorescence-based RT-PCR version of the assay was developed for screening large numbers of specimens. A large number of samples collected from wild birds was tested, resulting in the detection of avian paramyxoviruses type 1 in both barnacle and white-fronted geese, and type 8 in barnacle geese. Avian metapneumovirus type C was found for the first time in Europe in mallards, greylag geese and common gulls. The single round family-wide RT-PCR assay described here is a useful tool for the detection of known and unknown paramyxoviruses, and screening of large sample collections from humans and animals.

  6. Poecilia picta, a Close Relative to the Guppy, Exhibits Red Male Coloration Polymorphism: A System for Phylogenetic Comparisons.

    Science.gov (United States)

    Lindholm, Anna K; Sandkam, Ben; Pohl, Kristina; Breden, Felix

    2015-01-01

    Studies on the evolution of female preference and male color polymorphism frequently focus on single species since traits and preferences are thought to co-evolve. The guppy, Poecilia reticulata, has long been a premier model for such studies because female preferences and orange coloration are well known to covary, especially in upstream/downstream pairs of populations. However, focused single species studies lack the explanatory power of the comparative method, which requires detailed knowledge of multiple species with known evolutionary relationships. Here we describe a red color polymorphism in Poecilia picta, a close relative to guppies. We show that this polymorphism is restricted to males and is maintained in natural populations of mainland South America. Using tests of female preference we show female P. picta are not more attracted to red males, despite preferences for red/orange in closely related species, such as P. reticulata and P. parae. Male color patterns in these closely related species are different from P. picta in that they occur in discrete patches and are frequently Y chromosome-linked. P. reticulata have an almost infinite number of male patterns, while P. parae males occur in discrete morphs. We show the red male polymorphism in P. picta extends continuously throughout the body and is not a Y-linked trait despite the theoretical prediction that sexually-selected characters should often be linked to the heterogametic sex chromosome. The presence/absence of red male coloration of P. picta described here makes this an ideal system for phylogenetic comparisons that could reveal the evolutionary forces maintaining mate choice and color polymorphisms in this speciose group.

  7. Combining morphology, DNA sequences, and morphometrics: revising closely related species in the orb-weaving spider genus Araniella (Araneae, Araneidae).

    Science.gov (United States)

    Spasojevic, Tamara; Kropf, Christian; Nentwig, Wolfgang; Lasut, Liana

    2016-05-17

    The integration of independent data sets could solve problems in both traditional and DNA-based taxonomy. The aim of this study is to investigate the power of CO1 sequences and of morphometrics to distinguish closely related species in the spider genus Araniella. We put special emphasis on the species pair A. cucurbitina (Clerck, 1757) and A. opisthographa (Kulczyński, 1905) since the females are morphologically difficult to distinguish and often misidentified. A total of 216 sequences of eight Araniella species from seven European countries, North America and Asia were included in the molecular analysis. The results from both maximum likelihood and Bayesian phylogenetic inference indicate successful separation of six out of eight Araniella species, including A. cucurbitina and A. opisthographa. For the same six species, we detect no overlap of intra- and interspecific genetic divergence, leading to successful species identification with a threshold approach. In addition, morphometric analysis of the epigyna of A. cucurbitina and A. opisthographa supports species separation by two best explanatory ratios: receptaculum length and distance between receptaculum and copulatory duct. Although a small overlap in the ratios exists, the species identification rate increases when combining morphometric and molecular data, which demonstrates the efficiency of integrative approaches for distinguishing closely related species. However, none of the molecular approaches was able to separate closely related A. alpica (L. Koch, 1869) and A. inconspicua (Simon, 1874) due to shared CO1 haplotypes. Considering the clear morphological separation of the males and different habitat preferences, incomplete lineage sorting or introgressive hybridization could have led to identical CO1 sequences. Therefore, DNA-barcoding must be thoroughly tested even within small homogenous genera of spiders.

  8. Two closely related species of desert carpenter ant differ in individual-level allocation to fat storage.

    Science.gov (United States)

    Hahn, Daniel A

    2006-01-01

    Comparison of closely related species that differ in their life histories is a powerful method for studying the underlying physiological mechanisms contributing to life-history variation. I investigated whether two closely related members of the Camponotus festinatus species complex of desert carpenter ants, C. nr. festinatus Desert Light and C. nr. festinatus Desert Dark, differed in their life-history tactics with respect to fat storage. Newly mated queens were collected in the field, and colonies were reared under common conditions in the laboratory for 2 yr before sampling. I show that the two species differ in fat storage at the individual level. While the basic scaling relationship between lean mass and fat content did not differ between the two species, Dark workers and soldiers stored significantly more fat per unit lean mass than Light workers or soldiers. There were no significant demographic differences in the proportions of workers or soldiers involved in fat storage between the two species, although there was a trend toward Light colonies having a greater proportion of soldiers storing large amounts of fat. There was also no significant difference in the total amount of fat stored by the two species at the colony level. The detection of strong individual-level effects but no colony-level effects was likely due to the low statistical power of colony-level analyses. Showing that these two closely related species differ in fat storage at the individual level in a common environment demonstrates their utility as a model for understanding the physiological and behavioral mechanisms regulating life-history variation in fat storage in ants.

  9. The ectomycorrhizal morphotype Pinirhiza sclerotia is formed by Acephala macrosclerotiorum sp. nov., a close relative of Phialocephala fortinii.

    Science.gov (United States)

    Münzenberger, Babette; Bubner, Ben; Wöllecke, Jens; Sieber, Thomas N; Bauer, Robert; Fladung, Matthias; Hüttl, Reinhard F

    2009-09-01

    Relatively few ectomycorrhizal fungal species are known to form sclerotia. Usually, sclerotia are initiated at the extraradical mycelium. In this study, we present anatomical and ultrastructural evidence for the formation of sclerotia directly in the hyphal mantle of the mycorrhizal morphotype Pinirhiza sclerotia. A dark-pigmented fungal strain was isolated from Pinirhiza sclerotia and identified by molecular tools as Acephala macrosclerotiorum sp. nov., a close relative of Phialocephala fortinii s.l. As dark septate fungi are known to be mostly endophytic, resyntheses with Pinus sylvestris and A. macrosclerotiorum as well as Populus tremula x Populus tremuloides and A. macrosclerotiorum or P. fortinii s.l. were performed under axenic conditions. No mycorrhizas were found when hybrid aspen was inoculated with A. macrosclerotiorum or P. fortinii. However, A. macrosclerotiorum formed true ectomycorrhizas in vitro with P. sylvestris. Anatomical and ultrastructural features of this ectomycorrhiza are presented. The natural and synthesized ectomycorrhizal morphotypes were identical and characterized by a thin hyphal mantle that bore sclerotia in a later ontogenetic stage. The Hartig net was well-developed and grew up to the endodermis. To our knowledge, this is the first evidence at the anatomical and ultrastructural level that a close relative of P. fortinii s.l. forms true ectomycorrhizas with a coniferous host.

  10. Conservative whole-organ scaling contrasts with highly labile suborgan scaling differences among compound eyes of closely related Formica ants.

    Science.gov (United States)

    Perl, Craig D; Rossoni, Sergio; Niven, Jeremy E

    2017-03-01

    Static allometries determine how organ size scales in relation to body mass. The extent to which these allometric relationships are free to evolve, and how they differ among closely related species, has been debated extensively and remains unclear; changes in intercept appear common, but changes in slope are far rarer. Here, we compare the scaling relationships that govern the structure of compound eyes of four closely related ant species from the genus Formica. Comparison among these species revealed changes in intercept but not slope in the allometric scaling relationships governing eye area, facet number, and mean facet diameter. Moreover, the scaling between facet diameter and number was conserved across all four species. In contrast, facet diameters from distinct regions of the compound eye differed in both intercept and slope within a single species and when comparing homologous regions among species. Thus, even when species are conservative in the scaling of whole organs, they can differ substantially in regional scaling within organs. This, at least partly, explains how species can produce organs that adhere to genus wide scaling relationships while still being able to invest differentially in particular regions of organs to produce specific features that match their ecology.

  11. Antiviral Activity of Favipiravir (T-705) against a Broad Range of Paramyxoviruses In Vitro and against Human Metapneumovirus in Hamsters.

    Science.gov (United States)

    Jochmans, D; van Nieuwkoop, S; Smits, S L; Neyts, J; Fouchier, R A M; van den Hoogen, B G

    2016-08-01

    The clinical impact of infections with respiratory viruses belonging to the family Paramyxoviridae argues for the development of antiviral therapies with broad-spectrum activity. Favipiravir (T-705) has demonstrated potent antiviral activity against multiple RNA virus families and is presently in clinical evaluation for the treatment of influenza. Here we demonstrate in vitro activity of T-705 against the paramyxoviruses human metapneumovirus (HMPV), respiratory syncytial virus, human parainfluenza virus, measles virus, Newcastle disease virus, and avian metapneumovirus. In addition, we demonstrate activity against HMPV in hamsters. T-705 treatment inhibited replication of all paramyxoviruses tested in vitro, with 90% effective concentration (EC90) values of 8 to 40 μM. Treatment of HMPV-challenged hamsters with T-705 at 200 mg/kg of body weight/day resulted in 100% protection from infection of the lungs. In all treated and challenged animals, viral RNA remained detectable in the respiratory tract. The observation that T-705 treatment had a significant effect on infectious viral titers, with a limited effect on viral genome titers, is in agreement with its proposed mode of action of viral mutagenesis. However, next-generation sequencing of viral genomes isolated from treated and challenged hamsters did not reveal (hyper)mutation. Polymerase activity assays revealed a specific effect of T-705 on the activity of the HMPV polymerase. With the reported antiviral activity of T-705 against a broad range of RNA virus families, this small molecule is a promising broad-range antiviral drug candidate for limiting the viral burden of paramyxoviruses and for evaluation for treatment of infections with (re)emerging viruses, such as the henipaviruses.

  12. Isolation and characterisation of a ruminant alphaherpesvirus closely related to bovine herpesvirus 1 in a free-ranging red deer

    Directory of Open Access Journals (Sweden)

    Belák Sándor

    2007-09-01

    Full Text Available Abstract Background The genus Varicellovirus of the Herpesviridae subfamily Alphaherpesvirinae includes a cluster of viruses antigenically and genetically related to bovine herpesvirus 1 (BoHV-1: namely bovine herpesvirus 5 (BoHV-5, bubaline herpesvirus 1 (BuHV-1, caprine herpesvirus 1 (CpHV-1, cervid herpesviruses 1 (CvHV-1 and 2 (CvHV-2 and elk herpesvirus 1 (ElkHV-1. Considering the serological relationship between these ruminant alphaherpesviruses, several surveys have studied the occurrence of BoHV-1 related virus infection in wild and domestic ruminant species. In this way, a recent investigation has indicated, in Belgium, a high increase in the serological prevalence of BoHV-1 related virus infection in free-ranging red deer population. In this context, it has been decided to investigate the presence of an alphaherpesvirus spreading in the Belgian free-ranging red deer population. Results The current study reports the first isolation in a free-ranging red deer of a BoHV-1 closely related virus. The isolate was antigenically, genomically and genetically characterised by comparison with several ruminant alphaherpesvirus. Immunofluorescence assays revealed the isolate was antigenically distinct from bovine and caprine alphaherpesviruses. Similarly, BamHI and BstEII restriction analyses demonstrated the genomic difference between the isolate and the other ruminant alphaherpesviruses. Next, the sequencing of selected parts of UL27 and US8 genes showed a high degree of homologies between each BoHV-1 related ruminant alphaherpesvirus and the isolate. Besides the close relationship between all ruminant alphaherpesviruses, the phylogenetic analysis revealed that the isolate clustered with CvHV-1. Conclusion The first isolation of a virus closely related to BoHV-1 in a free-ranging red deer is reported. Data demonstrate that a CvHV-1 strain, named Anlier, circulates in wild red deer in continental Europe. Anlier strain show consistent differences

  13. Strong differences in chemical recognition cues between two closely related species of ants from the genus Lasius (Hymenoptera: Formicidae).

    Science.gov (United States)

    Morrison, W R; Witte, V

    2011-11-01

    Cuticular hydrocarbons (CHCs) are increasingly recognized as important to insects and are used for constructing taxonomies. However, multiple parameters affect the expression of CHCs besides a genetic component. We propose that selection may act differently on the expression of CHCs, depending on the evolutionary context. To explore the influence of selection, the CHCs of two closely related ant species, Lasius niger and Lasius platythorax, were studied in a multidisciplinary approach. We characterized (i) CHCs and (ii) niches (through baiting, activity observations and foraging analysis). The species were distinct in both measures, although to a varying degree. Although they showed moderate niche partitioning along diet and environmental preferences, chemical differences were unexpectedly pronounced. This may be explained by divergent selection on mate recognition cues or by other influences on CHCs. Such striking chemical differences among closely related species may not be the rule and suggest that taxonomies based on CHCs should be interpreted cautiously; though, they remain useful tools for differentiating among cryptic species. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  14. Molecular survey and characterization of a novel Anaplasma species closely related to Anaplasma capra in ticks, northwestern China.

    Science.gov (United States)

    Yang, Jifei; Liu, Zhijie; Niu, Qingli; Liu, Junlong; Han, Rong; Liu, Guangyuan; Shi, Yaoxu; Luo, Jianxun; Yin, Hong

    2016-11-25

    Anaplasma spp. are tick-transmitted bacteria that infect a wide variety of wild and domestic animals. These pathogens exhibit a high degree of biological diversity, broad geographical distribution, and represent a serious threat to veterinary and public health worldwide. A novel Anaplasma species was identified in Haemaphysalis qinghaiensis (Ixodidae) in northwestern China and was molecularly characterized by comparison of 16S rRNA, gltA, and groEL gene sequences. Of the 414 samples tested, 24 (5.8%) were positive for this Anaplasma species. On the basis of the 16S rRNA gene, this organism has been found to be closely related to and exhibit the highest sequence similarity with A. capra (99.8-99.9%) that was identified in goats and humans in northern China, but was distinct from other known Anaplasma species. Sequence analysis of the gltA and groEL genes revealed that this Anaplasma species was distinct from A. capra considering the lower sequence identity (88.6-88.7% for gltA and 90.6-91.0% for groEL) and a divergent phylogenetic position. Therefore, we described this Anaplasma species as A. capra-like bacteria. The present study reports a potential novel Anaplasma species closely related to A. capra in H. qinghaiensis in northwestern China. The zoonotic potential of A. capra-like bacteria needs to be further determined.

  15. Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.

    Science.gov (United States)

    Pei, Nancai; Erickson, David L; Chen, Bufeng; Ge, Xuejun; Mi, Xiangcheng; Swenson, Nathan G; Zhang, Jin-Long; Jones, Frank A; Huang, Chun-Lin; Ye, Wanhui; Hao, Zhanqing; Hsieh, Chang-Fu; Lum, Shawn; Bourg, Norman A; Parker, John D; Zimmerman, Jess K; McShea, William J; Lopez, Ida C; Sun, I-Fang; Davies, Stuart J; Ma, Keping; Kress, W John

    2015-10-12

    To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.

  16. Coagulation and fibrinolysis in capybara (Hydrochaeris hydrochaeris), a close relative of the guinea-pig (Cavia porcellus).

    Science.gov (United States)

    Leitão, D P; Polizello, A C; Rothschild, Z

    2000-01-01

    Fibrinolytic and coagulation properties of capybara (Hydrochaeris hydrochaeris, LINNAEUS, 1766) plasma were analysed and the results compared to the guinea-pig (Cavia porcellus), a close relative. Capybara fibrinogen was isolated and fibrinolysis of its plasma was carried out in a homologous system and with bovine fibrin. Undiluted plasma did not have fibrinolytic activity on fibrin plates; euglobulins gave a dose-related response. Zymography of capybara and guinea-pig plasma gave the same patterns of activity as human or bovine plasma. Human urokinase (UK) and tissue plasminogen activator (t-PA) produced lysis in capybara fibrin plates. Streptokinase (SK) (500 IU/ml) did not activate capybara or guinea-pig plasma. In this system, human plasma was extensively activated. Coagulation tests for both species of rodent were prolonged. The capybara showed values for prothrombin time (PT) shorter than activated thromboplastin time (APTT). The guinea-pig, as already shown, had longer PT values. Factors X and VII were very low for capybara and guinea-pig when tested using reference curves and diagnostic kits for human plasma. It is suggested that the capybara could be a valuable laboratory animal considering its size and closeness to the guinea-pig, and this could allow for the provision of materials from one single animal when convenient or necessary.

  17. Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?

    Energy Technology Data Exchange (ETDEWEB)

    Rivas-Ubach, Albert [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland Washington 99354 USA; CREAF, Cerdanyola del Vallès 08913 Catalonia Spain; Hódar, José A. [Grupo de Ecología Terrestre, Departamento de Biología Animal y Ecología, Facultad de Ciencias, Universidad de Granada, 18071 Granada Spain; Sardans, Jordi [CREAF, Cerdanyola del Vallès 08913 Catalonia Spain; CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès 08913 Catalonia Spain; Kyle, Jennifer E. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland Washington 99354 USA; Kim, Young-Mo [Biological Sciences Division, Pacific Northwest National Laboratory, Richland Washington 99354 USA; Oravec, Michal [Global Change Research Centre, Academy of Sciences of the Czech Republic, Bĕlidla 4a CZ-603 00 Brno Czech Republic; Urban, Otmar [Global Change Research Centre, Academy of Sciences of the Czech Republic, Bĕlidla 4a CZ-603 00 Brno Czech Republic; Guenther, Alex [Department of Earth System Science, University of California, Irvine California 92697 USA; Peñuelas, Josep [CREAF, Cerdanyola del Vallès 08913 Catalonia Spain; CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès 08913 Catalonia Spain

    2016-06-02

    The debate whether the coevolution of plants and insects or macroevolutionary processes (phylogeny) is the main driver determining the arsenal of molecular defensive compounds of plants remains unresolved. Attacks by herbivorous insects affect not only the composition of defensive compounds in plants but the entire metabolome (the set of molecular metabolites), including defensive compounds. Metabolomes are the final products of genotypes and are directly affected by macroevolutionary processes, so closely related species should have similar metabolomic compositions and may respond in similar ways to attacks by folivores. We analyzed the elemental compositions and metabolomes of needles from Pinus pinaster, P. nigra and P. sylvestris to determine if these closely related Pinus species with different coevolutionary histories with the caterpillars of the processionary moth respond similarly to attacks by this lepidopteran. All pines had different metabolomes and metabolic responses to herbivorous attack. The metabolomic variation among the pine species and the responses to folivory reflected their macroevolutionary relationships, with P. pinaster having the most divergent metabolome. The concentrations of phenolic metabolites were generally not higher in the attacked trees, which had lower concentrations of terpenes, suggesting that herbivores avoid individuals with high concentrations of terpenes. Our results suggest that macroevolutionary history plays important roles in the metabolomic responses of these pine species to folivory, but plant-insect coevolution probably constrains those responses. Combinations of different evolutionary factors and trade-offs are likely responsible for the different responses of each species to folivory, which is not necessarily exclusively linked to plant-insect coevolution.

  18. DNA barcoding in closely related species: A case study of Primula L.sect.Proliferae Pax (Primulaceae) in China

    Institute of Scientific and Technical Information of China (English)

    Hai-Fei YAN; Gang HAO; Chi-Ming HU; Xue-Jun GE

    2011-01-01

    DNA barcoding is a method of identifying species by analyzing one or a few short standardized DNA sequences. There are particular challenges in barcoding plants, especially for distinguishing closely related species. Hence, there is an urgent need to evaluate the performance of candidate loci for distinguishing between species, especially closely related species, to complement the rbcL + matK combination suggested as the core barcode for land plants. We sampled 48 individuals representing 12 species in Primula sect. Proliferae Pax in China to evaluate the performance of eight leading candidate barcode loci (matK, rbcL, rpoB, rpoCl, trnH-psbA, psbK-psbI, atpFatpH, and internal transcribed spacer (ITS)). The core combination rbcL + matK gave only 50% species resolution in sect. Proliferae. In terms of intraspecies and interspecies divergence, degree of monophyly, and sequence similarity, ITS, trnH-psbA, and psbK-psbI showed good performance as single-locus barcodes. Internal transcribed spacer displayed the highest genetic divergence and best discriminatory power, both alone and in combination with rbcL +matK (83.3% species resolution). We recommend evaluating the use of ITS for barcoding in other species. Low or single copy nuclear regions would provide more sophisticated barcoding tools in the long term, even though further research is required to find suitable loci.

  19. Bacillus Strains Most Closely Related to Bacillus nealsonii Are Not Effectively Circumscribed within the Taxonomic Species Definition

    Directory of Open Access Journals (Sweden)

    K. Kealy Peak

    2011-01-01

    Full Text Available Bacillus strains with >99.7% 16S rRNA gene sequence similarity were characterized with DNA:DNA hybridization, cellular fatty acid (CFA analysis, and testing of 100 phenotypic traits. When paired with the most closely related type strain, percent DNA:DNA similarities (% S for six Bacillus strains were all far below the recommended 70% threshold value for species circumscription with Bacillus nealsonii. An apparent genomic group of four Bacillus strain pairings with 94%–70% S was contradicted by the failure of the strains to cluster in CFA- and phenotype-based dendrograms as well as by their differentiation with 9–13 species level discriminators such as nitrate reduction, temperature range, and acid production from carbohydrates. The novel Bacillus strains were monophyletic and very closely related based on 16S rRNA gene sequence. Coherent genomic groups were not however supported by similarly organized phenotypic clusters. Therefore, the strains were not effectively circumscribed within the taxonomic species definition.

  20. Evolution of hydraulic traits in closely related species pairs from Mediterranean and nonMediterranean environments of North America.

    Science.gov (United States)

    Bhaskar, Radika; Valiente-Banuet, Alfonso; Ackerly, David D

    2007-01-01

    Chaparral shrubs in California experience cool, wet winters and hot, dry summers characteristic of mediterranean-type climates; by contrast, morphologically similar close relatives in central Mexico experience summer rainfall. A comparison of closely related species pairs was conducted to examine whether evolutionary divergences in plant hydraulic conductivity were associated with contrasting seasonality of precipitation. Six species pairs in Santa Barbara, California and Tehuacan, Mexico were chosen to test for repeated directional divergences across the habitat contrast. Additionally, evolutionary correlations were examined using phylogenetically independent contrasts (PICs) among a suite of hydraulic traits, including stem- and leaf-specific conductivity, resistance to embolism, wood density, inverse Huber value, and minimum seasonal water potential. Leaf-specific conductivity was generally higher in California, but for most hydraulic traits the species pairs exhibited varied evolutionary trajectories across the climate contrast. A significant correlation was found between divergences in xylem resistance to embolism and minimum seasonal water potential, but no evolutionary trade-off was found between resistance and stem conductivity. Higher leaf-specific conductivity may be adaptive in California, where soil and atmospheric droughts coincide during summer months. This response is consistent with a hydraulic strategy of high leaf water supply under high evaporative demand to prevent excessive drops in water potential.

  1. Posttraumatic Stress Disorder After Bereavement: Early Psychological Sequelae of Losing a Close Relative Due to Terminal Cancer

    DEFF Research Database (Denmark)

    Kristensen, T. E.; Elklit, A.; Karstoft, K. I.

    2012-01-01

    Very few studies have investigated posttraumatic stress disorder (PTSD) as a consequence of bereavement from terminal illness. Therefore, knowledge on the traumatizing effects of bereavement and risk factors for traumatization from bereavement is rather sparse. This study investigated prevalence...... and predictors of PTSD in a group of people who had recently lost a close relative due to incurable cancer. The participants were 132 persons who were assessed with the Harvard Trauma Questionnaire, the Trauma Symptom Checklist, and the Crisis Support Scale. One month after the loss, 29.5% of the subjects had...... clinical PTSD and an additional 26.2% reached a subclinical PTSD level. Negative affectivity, social support, and locus of control in relation to the loss predicted 57% of the variance in PTSD severity. A focus on these risk factors in early assessment after bereavement will help identify subjects at risk...

  2. The Cost of Mating: Influences of Life History Traits and Mating Strategies on Lifespan in Two Closely Related Yponomeuta Species

    Directory of Open Access Journals (Sweden)

    A. C. Bakker

    2011-01-01

    Full Text Available Theory predicts that in monandrous butterfly species males should not invest in a long lifespan because receptive females quickly disappear from the mating population. In polyandrous species, however, it pays for males to invest in longevity, which increases the number of mating opportunities and thus reproductive fitness. We tested an extension of this idea and compared male and female lifespan of two closely related Yponomeuta species with different degree of polyandry. Our results confirmed the theoretical prediction that male lifespan is fine-tuned to female receptive lifespan; once-mated males and females of both polyandrous species had an equal lifespan. However, the degree of polyandry was not reflected in male relative to female lifespan. The observed similar female and male lifespan could largely be attributed to a dramatic reduction of female lifespan after mating.

  3. Experimental infection of hamsters with avian paramyxovirus serotypes 1 to 9

    Directory of Open Access Journals (Sweden)

    Samuel Arthur S

    2011-02-01

    Full Text Available Abstract Avian paramyxoviruses (APMVs are frequently isolated from domestic and wild birds throughout the world and are separated into nine serotypes (APMV-1 to -9. Only in the case of APMV-1, the infection of non-avian species has been investigated. The APMVs presently are being considered as human vaccine vectors. In this study, we evaluated the replication and pathogenicity of all nine APMV serotypes in hamsters. The hamsters were inoculated intranasally with each virus and monitored for clinical disease, pathology, histopathology, virus replication, and seroconversion. On the basis of one or more of these criteria, each of the APMV serotypes was found to replicate in hamsters. The APMVs produced mild or inapparent clinical signs in hamsters except for APMV-9, which produced moderate disease. Gross lesions were observed over the pulmonary surface of hamsters infected with APMV-2 & -3, which showed petechial and ecchymotic hemorrhages, respectively. Replication of all of the APMVs except APMV-5 was confirmed in the nasal turbinates and lungs, indicating a tropism for the respiratory tract. Histologically, the infection resulted in lung lesions consistent with bronchointerstitial pneumonia of varying severity and nasal turbinates with blunting or loss of cilia of the epithelium lining the nasal septa. The majority of APMV-infected hamsters exhibited transient histological lesions that self resolved by 14 days post infection (dpi. All of the hamsters infected with the APMVs produced serotype-specific HI or neutralizing antibodies, confirming virus replication. Taken together, these results demonstrate that all nine known APMV serotypes are capable of replicating in hamsters with minimal disease and pathology.

  4. Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus)

    Science.gov (United States)

    Dimitrov, Kiril M.; Ramey, Andy M.; Qiu, Xueting; Bahl, Justin; Afonso, Claudio L.

    2016-01-01

    Newcastle disease is caused by virulent forms of avian paramyxovirus of serotype 1 (APMV-1) and has global economic importance. The disease reached panzootic proportions within two decades after first being identified in 1926 in the United Kingdom and Indonesia and still remains endemic in many countries across the world. Here we review information on the host, temporal, and geographic distribution of APMV-1 genetic diversity based on the evolutionary systematics of the complete coding region of the fusion gene. Strains of APMV-1 are phylogenetically separated into two classes (class I and class II) and further classified into genotypes based on genetic differences. Class I viruses are genetically less diverse, generally present in wild waterfowl, and are of low virulence. Class II viruses are genetically and phenotypically more diverse, frequently isolated from poultry with occasional spillovers into wild birds, and exhibit a wider range of virulence. Waterfowl, cormorants, and pigeons are natural reservoirs of all APMV-1 pathotypes, except viscerotropic velogenic viruses for which natural reservoirs have not been identified. Genotypes I and II within class II include isolates of high and low virulence, the latter often being used as vaccines. Viruses of genotypes III and IX that emerged decades ago are now isolated rarely, but may be found in domestic and wild birds in China. Containing only virulent viruses and responsible for the majority of recent outbreaks in poultry and wild birds, viruses from genotypes V, VI, and VII, are highly mobile and have been isolated on different continents. Conversely, virulent viruses of genotypes XI (Madagascar), XIII (mainly Southwest Asia), XVI (North America) and XIV, XVII and XVIII (Africa) appear to have a more limited geographic distribution and have been isolated predominantly from poultry.

  5. Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus).

    Science.gov (United States)

    Dimitrov, Kiril M; Ramey, Andrew M; Qiu, Xueting; Bahl, Justin; Afonso, Claudio L

    2016-04-01

    Newcastle disease is caused by virulent forms of avian paramyxovirus of serotype 1 (APMV-1) and has global economic importance. The disease reached panzootic proportions within two decades after first being identified in 1926 in the United Kingdom and Indonesia and still remains endemic in many countries across the world. Here we review information on the host, temporal, and geographic distribution of APMV-1 genetic diversity based on the evolutionary systematics of the complete coding region of the fusion gene. Strains of APMV-1 are phylogenetically separated into two classes (class I and class II) and further classified into genotypes based on genetic differences. Class I viruses are genetically less diverse, generally present in wild waterfowl, and are of low virulence. Class II viruses are genetically and phenotypically more diverse, frequently isolated from poultry with occasional spillovers into wild birds, and exhibit a wider range of virulence. Waterfowl, cormorants, and pigeons are natural reservoirs of all APMV-1 pathotypes, except viscerotropic velogenic viruses for which natural reservoirs have not been identified. Genotypes I and II within class II include isolates of high and low virulence, the latter often being used as vaccines. Viruses of genotypes III and IX that emerged decades ago are now isolated rarely, but may be found in domestic and wild birds in China. Containing only virulent viruses and responsible for the majority of recent outbreaks in poultry and wild birds, viruses from genotypes V, VI, and VII, are highly mobile and have been isolated on different continents. Conversely, virulent viruses of genotypes XI (Madagascar), XIII (mainly Southwest Asia), XVI (North America) and XIV, XVII and XVIII (Africa) appear to have a more limited geographic distribution and have been isolated predominantly from poultry.

  6. Replication, neurotropism, and pathogenicity of avian paramyxovirus serotypes 1-9 in chickens and ducks.

    Directory of Open Access Journals (Sweden)

    Shin-Hee Kim

    Full Text Available Avian paramyxovirus (APMV serotypes 1-9 have been isolated from many different avian species. APMV-1 (Newcastle disease virus is the only well-characterized serotype, because of the high morbidity, mortality, and economic loss caused by highly virulent strains. Very little is known about the pathogenesis, replication, virulence, and tropism of the other APMV serotypes. Here, this was evaluated for prototypes strains of APMV serotypes 2-9 in cell culture and in chickens and ducks. In cell culture, only APMV-1, -3 and -5 induced syncytium formation. In chicken DF1 cells, APMV-3 replicated with an efficiency approaching that of APMV-1, while APMV-2 and -5 replicated to lower, intermediate titers and the others were much lower. Mean death time (MDT assay in chicken eggs and intracerebral pathogenicity index (ICPI test in 1-day-old SPF chicks demonstrated that APMV types 2-9 were avirulent. Evaluation of replication in primary neuronal cells in vitro as well as in the brains of 1-day-old chicks showed that, among types 2-9, only APMV-3 was neurotropic, although this virus was not neurovirulent. Following intranasal infection of 1-day-old and 2-week-old chickens, replication of APMV types 2-9 was mostly restricted to the respiratory tract, although APMV-3 was neuroinvasive and neurotropic (but not neurovirulent and also was found in the spleen. Experimental intranasal infection of 3-week-old mallard ducks with the APMVs did not produce any clinical signs (even for APMV-1 and exhibited restricted viral replication of the APMVs (including APMV-1 to the upper respiratory tract regardless of their isolation source, indicating avirulence of APMV types 1-9 in mallard ducks. The link between the presence of a furin cleavage site in the F protein, syncytium formation, systemic spread, and virulence that has been well-established with APMV-1 pathotypes was not evident with the other APMV serotypes.

  7. ”How do the patients and their close relatives experience The Coordinated Investigation Model of Dementia in the North Denmark Region?”

    DEFF Research Database (Denmark)

    Hulgaard, Hanne; Ottesen, Aase Marie

    How do the patients and their close relatives experience The Coordinated Investigation Model of Dementia in the North Denmark Region? The aim of the project was to investigate how the patients and their close relatives experienced the investigation and the subsequent social medicine intervention...

  8. Organellar Genomes from a ∼5,000-Year-Old Archaeological Maize Sample Are Closely Related to NB Genotype

    Science.gov (United States)

    Pérez-Zamorano, Bernardo; Vallebueno-Estrada, Miguel; Martínez González, Javier; García Cook, Angel; Montiel, Rafael; Vielle-Calzada, Jean-Philippe

    2017-01-01

    The story of how preColumbian civilizations developed goes hand-in-hand with the process of plant domestication by Mesoamerican inhabitants. Here, we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacán, México. Accelerator mass spectrometry dated the maize sample to be 5,040–5,300 years before present (95% probability). Phylogenetic analysis of the mitochondrial genome shows that the archaeological sample branches basal to the other Zea mays genomes, as expected. However, this analysis also indicates that fertile genotype NB is closely related to the archaeological maize sample and evolved before cytoplasmic male sterility genotypes (CMS-S, CMS-T, and CMS-C), thus contradicting previous phylogenetic analysis of mitochondrial genomes from maize. We show that maximum-likelihood infers a tree where CMS genotypes branch at the base of the tree when including sites that have a relative fast rate of evolution thus suggesting long-branch attraction. We also show that Bayesian analysis infer a topology where NB and the archaeological maize sample are at the base of the tree even when including faster sites. We therefore suggest that previous trees suffered from long-branch attraction. We also show that the phylogenetic analysis of the ancient chloroplast is congruent with genotype NB to be more closely related to the archaeological maize sample. As shown here, the inclusion of ancient genomes on phylogenetic trees greatly improves our understanding of the domestication process of maize, one of the most important crops worldwide. PMID:28338960

  9. Vibrio vulnificus phage PV94 is closely related to temperate phages of V. cholerae and other Vibrio species.

    Science.gov (United States)

    Pryshliak, Mark; Hammerl, Jens A; Reetz, Jochen; Strauch, Eckhard; Hertwig, Stefan

    2014-01-01

    Vibrio vulnificus is an important pathogen which can cause serious infections in humans. Yet, there is limited knowledge on its virulence factors and the question whether temperate phages might be involved in pathogenicity, as is the case with V. cholerae. Thus far, only two phages (SSP002 and VvAW1) infecting V. vulnificus have been genetically characterized. These phages were isolated from the environment and are not related to Vibrio cholerae phages. The lack of information on temperate V. vulnificus phages prompted us to isolate those phages from lysogenic strains and to compare them with phages of other Vibrio species. In this study the temperate phage PV94 was isolated from a V. vulnificus biotype 1 strain by mitomycin C induction. PV94 is a myovirus whose genome is a linear double-stranded DNA of 33,828 bp with 5'-protruding ends. Sequence analysis of PV94 revealed a modular organization of the genome. The left half of the genome comprising the immunity region and genes for the integrase, terminase and replication proteins shows similarites to V. cholerae kappa phages whereas the right half containing genes for structural proteins is closely related to a prophage residing in V. furnissii NCTC 11218. We present the first genomic sequence of a temperate phage isolated from a human V. vulnificus isolate. The sequence analysis of the PV94 genome demonstrates the wide distribution of closely related prophages in various Vibrio species. Moreover, the mosaicism of the PV94 genome indicates a high degree of horizontal genetic exchange within the genus Vibrio, by which V. vulnificus might acquire virulence-associated genes from other species.

  10. Vibrio vulnificus phage PV94 is closely related to temperate phages of V. cholerae and other Vibrio species.

    Directory of Open Access Journals (Sweden)

    Mark Pryshliak

    Full Text Available BACKGROUND: Vibrio vulnificus is an important pathogen which can cause serious infections in humans. Yet, there is limited knowledge on its virulence factors and the question whether temperate phages might be involved in pathogenicity, as is the case with V. cholerae. Thus far, only two phages (SSP002 and VvAW1 infecting V. vulnificus have been genetically characterized. These phages were isolated from the environment and are not related to Vibrio cholerae phages. The lack of information on temperate V. vulnificus phages prompted us to isolate those phages from lysogenic strains and to compare them with phages of other Vibrio species. RESULTS: In this study the temperate phage PV94 was isolated from a V. vulnificus biotype 1 strain by mitomycin C induction. PV94 is a myovirus whose genome is a linear double-stranded DNA of 33,828 bp with 5'-protruding ends. Sequence analysis of PV94 revealed a modular organization of the genome. The left half of the genome comprising the immunity region and genes for the integrase, terminase and replication proteins shows similarites to V. cholerae kappa phages whereas the right half containing genes for structural proteins is closely related to a prophage residing in V. furnissii NCTC 11218. CONCLUSION: We present the first genomic sequence of a temperate phage isolated from a human V. vulnificus isolate. The sequence analysis of the PV94 genome demonstrates the wide distribution of closely related prophages in various Vibrio species. Moreover, the mosaicism of the PV94 genome indicates a high degree of horizontal genetic exchange within the genus Vibrio, by which V. vulnificus might acquire virulence-associated genes from other species.

  11. Specificity of herbivore-induced hormonal signaling and defensive traits in five closely related milkweeds (Asclepias spp.).

    Science.gov (United States)

    Agrawal, Anurag A; Hastings, Amy P; Patrick, Eamonn T; Knight, Anna C

    2014-07-01

    Despite the recognition that phytohormonal signaling mediates induced responses to herbivory, we still have little understanding of how such signaling varies among closely related species and may generate herbivore-specific induced responses. We studied closely related milkweeds (Asclepias) to link: 1) plant damage by two specialist chewing herbivores (milkweed leaf beetles Labidomera clivicolis and monarch caterpillars Danaus plexippus); 2) production of the phytohormones jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA); 3) induction of defensive cardenolides and latex; and 4) impacts on Danaus caterpillars. We first show that A. syriaca exhibits induced resistance following monarch herbivory (i.e., reduced monarch growth on previously damaged plants), while the defensively dissimilar A. tuberosa does not. We next worked with a broader group of five Asclepias, including these two species, that are highly divergent in defensive traits yet from the same clade. Three of the five species showed herbivore-induced changes in cardenolides, while induced latex was found in four species. Among the phytohormones, JA and ABA showed specific responses (although they generally increased) to insect species and among the plant species. In contrast, SA responses were consistent among plant and herbivore species, showing a decline following herbivore attack. Jasmonic acid showed a positive quantitative relationship only with latex, and this was strongest in plants damaged by D. plexippus. Although phytohormones showed qualitative tradeoffs (i.e., treatments that enhanced JA reduced SA), the few significant individual plant-level correlations among hormones were positive, and these were strongest between JA and ABA in monarch damaged plants. We conclude that: 1) latex exudation is positively associated with endogenous JA levels, even among low-latex species; 2) correlations among milkweed hormones are generally positive, although herbivore damage induces a

  12. New Techniques for Relating Dynamically Close Galaxy Pairs to Merger and Accretion Rates Application to the SSRS2 Redshift Survey

    CERN Document Server

    Patton, D R; Marzke, R O; Pritchet, C J; Da Costa, L N; Pellegrini, P S

    2000-01-01

    We introduce two new pair statistics, which relate close galaxy pairs to the merger and accretion rates. We demonstrate the importance of correcting these (and other) pair statistics for selection effects related to sample depth and completeness. In particular, we highlight the severe bias that can result from the use of a flux-limited survey. The first statistic, denoted N_c, gives the number of companions per galaxy, within a specified range in absolute magnitude. N_c is directly related to the galaxy merger rate. The second statistic, called L_c, gives the total luminosity in companions, per galaxy. This quantity can be used to investigate the mass accretion rate. Both N_c and L_c are related to the galaxy correlation function and luminosity function in a straightforward manner. We outline techniques which account for various selection effects, and demonstrate the success of this approach using Monte Carlo simulations. If one assumes that clustering is independent of luminosity (which is appropriate for re...

  13. Mesophyll cells of C4 plants have fewer chloroplasts than those of closely related C3 plants.

    Science.gov (United States)

    Stata, Matt; Sage, Tammy L; Rennie, Troy D; Khoshravesh, Roxana; Sultmanis, Stefanie; Khaikin, Yannay; Ludwig, Martha; Sage, Rowan F

    2014-11-01

    The evolution of C(4) photosynthesis from C(3) ancestors eliminates ribulose bisphosphate carboxylation in the mesophyll (M) cell chloroplast while activating phosphoenolpyruvate (PEP) carboxylation in the cytosol. These changes may lead to fewer chloroplasts and different chloroplast positioning within M cells. To evaluate these possibilities, we compared chloroplast number, size and position in M cells of closely related C(3), C(3) -C(4) intermediate and C(4) species from 12 lineages of C(4) evolution. All C(3) species had more chloroplasts per M cell area than their C(4) relatives in high-light growth conditions. C(3) species also had higher chloroplast coverage of the M cell periphery than C(4) species, particularly opposite intercellular air spaces. In M cells from 10 of the 12 C(4) lineages, a greater fraction of the chloroplast envelope was pulled away from the plasmalemma in the C(4) species than their C(3) relatives. C(3) -C(4) intermediate species generally exhibited similar patterns as their C(3) relatives. We interpret these results to reflect adaptive shifts that facilitate efficient C(4) function by enhancing diffusive access to the site of primary carbon fixation in the cytosol. Fewer chloroplasts in C(4) M cells would also reduce shading of the bundle sheath chloroplasts, which also generate energy required by C(4) photosynthesis.

  14. Different mechanics of snap-trapping in the two closely related carnivorous plants Dionaea muscipula and Aldrovanda vesiculosa

    Science.gov (United States)

    Poppinga, Simon; Joyeux, Marc

    2011-10-01

    The carnivorous aquatic waterwheel plant (Aldrovanda vesiculosa L.) and the closely related terrestrial venus flytrap (Dionaea muscipula Sol. ex J. Ellis) both feature elaborate snap-traps, which shut after reception of an external mechanical stimulus by prey animals. Traditionally, Aldrovanda is considered as a miniature, aquatic Dionaea, an assumption which was already established by Charles Darwin. However, videos of snapping traps from both species suggest completely different closure mechanisms. Indeed, the well-described snapping mechanism in Dionaea comprises abrupt curvature inversion of the two trap lobes, while the closing movement in Aldrovanda involves deformation of the trap midrib but not of the lobes, which do not change curvature. In this paper, we present detailed mechanical models for these plants, which are based on the theory of thin solid membranes and explain this difference by showing that the fast snapping of Aldrovanda is due to kinematic amplification of the bending deformation of the midrib, while that of Dionaea unambiguously relies on the buckling instability that affects the two lobes.

  15. Molecular dynamics analysis of conformational change of paramyxovirus F protein during the initial steps of membrane fusion

    Energy Technology Data Exchange (ETDEWEB)

    Martin-Garcia, Fernando; Mendieta-Moreno, Jesus Ignacio; Mendieta, Jesus [Centro de Biologia Molecular ' Severo Ochoa' (CSIC/UAM), C/ Nicolas Cabrera, 1, Cantoblanco, 28049 Madrid (Spain); Biomol-Informatics SL, Parque Cientifico de Madrid, C/ Faraday, 7, Cantoblanco, 28049 Madrid (Spain); Gomez-Puertas, Paulino, E-mail: pagomez@cbm.uam.es [Centro de Biologia Molecular ' Severo Ochoa' (CSIC/UAM), C/ Nicolas Cabrera, 1, Cantoblanco, 28049 Madrid (Spain)

    2012-03-30

    Highlights: Black-Right-Pointing-Pointer Initial conformational change of paramyxovirus F protein is caused only by mechanical forces. Black-Right-Pointing-Pointer HRA region undergoes a structural change from a beta + alpha conformation to an extended coil and then to an all-alpha conformation. Black-Right-Pointing-Pointer HRS domains of F protein form three single {alpha}-helices prior to generation of the coiled coil. -- Abstract: The fusion of paramyxovirus to the cell membrane is mediated by fusion protein (F protein) present in the virus envelope, which undergoes a dramatic conformational change during the process. Unlike hemagglutinin in orthomyxovirus, this change is not mediated by an alteration of environmental pH, and its cause remains unknown. Steered molecular dynamics analysis leads us to suggest that the conformational modification is mediated only by stretching mechanical forces once the transmembrane fusion peptide of the protein is anchored to the cell membrane. Such elongating forces will generate major secondary structure rearrangement in the heptad repeat A region of the F protein; from {beta}-sheet conformation to an elongated coil and then spontaneously to an {alpha}-helix. In addition, it is proposed that the heptad repeat A region adopts a final three-helix coiled coil and that this structure appears after the formation of individual helices in each monomer.

  16. Leave for illness/accident or in the event of illness of a close relative - New medical certificate templates

    CERN Multimedia

    HR department

    2016-01-01

    Medical certificate templates are now available in the Admin e-guide (follow the “Forms and templates” link):    Medical certificate for illness/accident Medical certificate for a medical examination or treatment Medical certificate in the event of illness of a close relative These templates are provided for the convenience of members of the personnel and their use is recommended but not compulsory. Other forms of medical certificates issued by a medical doctor may also be submitted, provided they contain the same items of information as those given in the templates. More information on the applicable rules and on the way leave is managed at CERN can be found in the Admin e-guide web pages. Human Resources department HR.leave@cern.ch

  17. Shedding dynamics of Morogoro virus, an African arenavirus closely related to Lassa virus, in its natural reservoir host Mastomys natalensis.

    Science.gov (United States)

    Borremans, Benny; Vossen, Raphaël; Becker-Ziaja, Beate; Gryseels, Sophie; Hughes, Nelika; Van Gestel, Mats; Van Houtte, Natalie; Günther, Stephan; Leirs, Herwig

    2015-05-29

    Arenaviruses can cause mild to severe hemorrhagic fevers. Humans mainly get infected through contact with infected rodents or their excretions, yet little is known about transmission dynamics within rodent populations. Morogoro virus (MORV) is an Old World arenavirus closely related to Lassa virus with which it shares the same host species Mastomys natalensis. We injected MORV in its host, and sampled blood and excretions at frequent intervals. Infection in adults was acute; viral RNA disappeared from blood after 18 days post infection (dpi) and from excretions after 39 dpi. Antibodies were present from 7 dpi and never disappeared. Neonatally infected animals acquired a chronic infection with RNA and antibodies in blood for at least 3 months. The quantified excretion and antibody patterns can be used to inform mathematical transmission models, and are essential for understanding and controlling transmission in the natural rodent host populations.

  18. [Genetic Connectivity Between Sympatric Populations of Closely Related Char Species, Dolly Varden Salvelinus malma and White Char Salvelinus albus].

    Science.gov (United States)

    Salmenkova, E A

    2016-01-01

    The closely related chars Salvelinus malma and Salvelinus albus, which sympatrically inhabit the Kamchatka River basin and Kronotsky Lake (Kamchatka), attract the attention of the researchers because of their debated origin and taxonomic status. Previous studies of sympatric populations of these chars revealed small but statistically significant genetic differences between these species at a number of molecular markers, suggesting the presence of the genetic exchange and hybridization. In this study, based on genotypic characterization of nine microsatellite loci, a considerable level of historical and contemporary genetic migration between sympatric populations of these chars was demonstrated. At the individual level a high degree of hybridization was observed, mainly among the Dolly Varden individuals from the studied populations. The obtained evidence on the genetic connectivity between sympatric S. malma and S. albus do not support the separate species status of S. albus.

  19. Mutations and/or close relatives? Six case work examples where 49 autosomal SNPs were used as supplementary markers.

    Science.gov (United States)

    Børsting, Claus; Morling, Niels

    2011-06-01

    Six case work examples are presented, where the individuals were typed for 15 autosomal short tandem repeats (STRs) and 49 autosomal single nucleotide polymorphisms (SNPs). The 15 STRs were typed with the AmpFlSTR Identifiler PCR Amplification Kit and the 49 SNPs were typed with the SNPforID multiplex assay. The six cases included two duos, two trios and two cases, where the alleged father was not available for testing and one or two of his close relatives were tested instead. The SNP investigation was more informative than the STR investigation in all six cases. In two cases, the alleged father would have been falsely included based on the STR results, while the SNP results showed that the alleged father was not the true parent. These case work examples underline the importance of performing supplementary investigations in selected cases and demonstrate the usefulness of the SNPforID multiplex assay.

  20. New species of Monepidosis Mamaev, 1966 and Antipodosis gen. nov., a closely related genus from New Zealand (Diptera, Cecidomyiidae

    Directory of Open Access Journals (Sweden)

    Mathias Jaschhof

    2016-04-01

    Full Text Available Three new species of Monepidosis Mamaev, 1966, a Holarctic genus of Porricondylinae (Diptera, Cecidomyiidae, are described: M. heterocera sp. nov. from Sweden and Germany, M. scepteroides sp. nov. from Sweden, and M. shikokuensis sp. nov. from Japan. A new porricondyline genus, Antipodosis gen. nov., is introduced for eight new species from New Zealand, named A. australis gen. et sp. nov., A. elongata gen. et sp. nov., A. granvillensis gen. et sp. nov., A. pureora gen. et sp. nov., A. rakiura gen. et sp. nov., A. rotoiti gen. et sp. nov., A. rotoroa gen. et sp. nov., and A. waipapa gen. et sp. nov. Male genitalic morphology indicates that Monepidosis and Antipodosis gen. nov. are closely related, together forming the Monepidosis group of genera, which stands out from the other Porricondylini. Monepidosis spatulata Spungis, 2006, a species originally described from Latvia and Lithuania, is for the first time reported to occur in Sweden.

  1. A comparative infection study of pigeon and avian paramyxovirus type 1 viruses in pigeons: Evaluation of clinical signs, virus shedding and seroconversion

    NARCIS (Netherlands)

    Dortmans, J.C.F.M.; Koch, G.; Rottier, P.J.M.; Peeters, B.P.H.

    2011-01-01

    The pathogenesis of pigeon paramyxovirus type 1 (PPMV-1) isolate AV324/96 and of its recombinant derivative, rgAV324, was studied in pigeons. For comparison, the virulent chicken virus FL-Herts, which is a recombinant derivative of strain Herts/33, was also included. After inoculation by the combine

  2. Similarity of avian paramyxovirus serotype 1 isolates of low virulence for chickens obtained from contaminated poultry vaccines and from poultry flocks

    DEFF Research Database (Denmark)

    Jørgensen, Poul Henrik; Handberg, K. J.; Ahrens, Peter;

    2000-01-01

    At present Denmark has the status of a 'non-vaccinating' country for Newcastle disease and its poultry population should therefore be free of antibodies to avian paramyxovirus 1 (APMV-1). Three live avian vaccines against infectious bronchitis, avian encephalomyelitis, and chick anaemia which had...

  3. Genetic data from avian influenza and avian paramyxoviruses generated by the European network of excellence (EPIZONE) between 2006 and 2011—Review and recommendations for surveillance

    DEFF Research Database (Denmark)

    Dundon, William G.; Heidari, Alireza; Fusaro, Alice

    2012-01-01

    Since 2006, the members of the molecular epidemiological working group of the European “EPIZONE” network of excellence have been generating sequence data on avian influenza and avian paramyxoviruses from both European and African sources in an attempt to more fully understand the circulation...

  4. Sampling strategy and potential utility of indels for DNA barcoding of closely related plant species: a case study in taxus.

    Science.gov (United States)

    Liu, Jie; Provan, Jim; Gao, Lian-Ming; Li, De-Zhu

    2012-01-01

    Although DNA barcoding has become a useful tool for species identification and biodiversity surveys in plant sciences, there remains little consensus concerning appropriate sampling strategies and the treatment of indels. To address these two issues, we sampled 39 populations for nine Taxus species across their entire ranges, with two to three individuals per population randomly sampled. We sequenced one core DNA barcode (matK) and three supplementary regions (trnH-psbA, trnL-trnF and ITS) for all samples to test the effects of sampling design and the utility of indels. Our results suggested that increasing sampling within-population did not change the clustering of individuals, and that meant within-population P-distances were zero for most populations in all regions. Based on the markers tested here, comparison of methods either including or excluding indels indicated that discrimination and nodal support of monophyletic groups were significantly increased when indels were included. Thus we concluded that one individual per population was adequate to represent the within-population variation in these species for DNA barcoding, and that intra-specific sampling was best focused on representing the entire ranges of certain taxa. We also found that indels occurring in the chloroplast trnL-trnF and trnH-psbA regions were informative to differentiate among for closely related taxa barcoding, and we proposed that indel-coding methods should be considered for use in future for closed related plant species DNA barcoding projects on or below generic level.

  5. 16S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads.

    Science.gov (United States)

    Tokajian, Sima; Issa, Nahla; Salloum, Tamara; Ibrahim, Joe; Farah, Maya

    2016-01-01

    Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S-23S rDNA intergenic spacer (ITS) sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S-23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 and 849 bp, while their G+C content was 42.2-57.9 mol%. Five distinct ITS types were identified: ITS(none) (without tRNA genes), ITS(Ala(TGC)), ITS(Ala(TGC)+Ile(GAT)), ITS(Ile(GAT)+Ala(TGC)), and ITS (Ile(GAT)+Pseudo). All of the identified tRNA(Ala(TGC)) molecules consisted of 73 bases, and all of the tRNA(Ile(GAT)) molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2. The importance of this study is that this is the first comparison of the 16S-23S rDNA ITS sequence similarities and tRNA genes from sphingomonads. Collectively the data obtained in this study revealed the heterogeneity and extent of variability within the ITS region compared to the 16S rRNA gene within closely related isolates. Sequence and length polymorphisms within the ITS region along with the ITS types (tRNA-containing or lacking and the type of tRNA) and ITS-2 size and sequence similarities allowed us to overcome the limitation we previously encountered in resolving closely related isolates based on the 16S rRNA gene sequence.

  6. Transcriptome sequencing of Crucihimalaya himalaica (Brassicaceae) reveals how Arabidopsis close relative adapt to the Qinghai-Tibet Plateau.

    Science.gov (United States)

    Qiao, Qin; Wang, Qia; Han, Xi; Guan, Yanlong; Sun, Hang; Zhong, Yang; Huang, Jinling; Zhang, Ticao

    2016-02-24

    The extreme environment of the Qinghai-Tibet Plateau (QTP) provides an ideal natural laboratory for studies on adaptive evolution. Few genome/transcriptome based studies have been conducted on how plants adapt to the environments of QTP compared to numerous studies on vertebrates. Crucihimalaya himalaica is a close relative of Arabidopsis with typical QTP distribution, and is hoped to be a new model system to study speciation and ecological adaptation in extreme environment. In this study, we de novo generated a transcriptome sequence of C. himalaica, with a total of 49,438 unigenes. Compared to five relatives, 10,487 orthogroups were shared by all six species, and 4,286 orthogroups contain putative single copy gene. Further analysis identified 487 extremely significantly positively selected genes (PSGs) in C. himalaica transcriptome. Theses PSGs were enriched in functions related to specific adaptation traits, such as response to radiation, DNA repair, nitrogen metabolism, and stabilization of membrane. These functions are responsible for the adaptation of C. himalaica to the high radiation, soil depletion and low temperature environments on QTP. Our findings indicate that C. himalaica has evolved complex strategies for adapting to the extreme environments on QTP and provide novel insights into genetic mechanisms of highland adaptation in plants.

  7. 29 CFR 776.17 - Employment in a “closely related process or occupation directly essential to” production of goods.

    Science.gov (United States)

    2010-07-01

    ... § 776.17 Employment in a “closely related process or occupation directly essential to” production of... process or occupation directly essential to the production thereof, in any State.” 77 Prior to the Fair... criteria for determining whether a process or occupation is “closely related” to production cannot...

  8. Characterization of a novel Lactobacillus species closely related to Lactobacillus johnsonii using a combination of molecular and comparative genomics methods

    Directory of Open Access Journals (Sweden)

    Pérez-Martínez Gaspar

    2010-09-01

    Full Text Available Abstract Background Comparative genomic hybridization (CGH constitutes a powerful tool for identification and characterization of bacterial strains. In this study we have applied this technique for the characterization of a number of Lactobacillus strains isolated from the intestinal content of rats fed with a diet supplemented with sorbitol. Results Phylogenetic analysis based on 16S rRNA gene, recA, pheS, pyrG and tuf sequences identified five bacterial strains isolated from the intestinal content of rats as belonging to the recently described Lactobacillus taiwanensis species. DNA-DNA hybridization experiments confirmed that these five strains are distinct but closely related to Lactobacillus johnsonii and Lactobacillus gasseri. A whole genome DNA microarray designed for the probiotic L. johnsonii strain NCC533 was used for CGH analysis of L. johnsonii ATCC 33200T, L. johnsonii BL261, L. gasseri ATCC 33323T and L. taiwanensis BL263. In these experiments, the fluorescence ratio distributions obtained with L. taiwanensis and L. gasseri showed characteristic inter-species profiles. The percentage of conserved L. johnsonii NCC533 genes was about 83% in the L. johnsonii strains comparisons and decreased to 51% and 47% for L. taiwanensis and L. gasseri, respectively. These results confirmed the separate status of L. taiwanensis from L. johnsonii at the level of species, and also that L. taiwanensis is closer to L. johnsonii than L. gasseri is to L. johnsonii. Conclusion Conventional taxonomic analyses and microarray-based CGH analysis have been used for the identification and characterization of the newly species L. taiwanensis. The microarray-based CGH technology has been shown as a remarkable tool for the identification and fine discrimination between phylogenetically close species, and additionally provided insight into the adaptation of the strain L. taiwanensis BL263 to its ecological niche.

  9. Vibrio metoecus sp. nov., a close relative of Vibrio cholerae isolated from coastal brackish ponds and clinical specimens.

    Science.gov (United States)

    Kirchberger, Paul C; Turnsek, Maryann; Hunt, Dana E; Haley, Bradd J; Colwell, Rita R; Polz, Martin F; Tarr, Cheryl L; Boucher, Yan

    2014-09-01

    A Gram-staining-negative, curved-rod-shaped bacterium with close resemblance to Vibrio cholerae, the aetiological agent of cholera, was isolated over the course of several years from coastal brackish water (17 strains) and from clinical cases (two strains) in the United States. 16S rRNA gene identity with V. cholerae exceeded 98 % yet an average nucleotide identity based on genome data of around 86 % and multi locus sequence analysis of six housekeeping genes (mdh, adk, gyrB, recA, pgi and rpoB) clearly delineated these isolates as a distinct genotypic cluster within the V. cholerae-V. mimicus clade. Most standard identification techniques do not differentiate this cluster of isolates from V. cholerae. Only amplification of the ompW gene using V. cholerae-specific primers and a negative Voges-Proskauer test showed a difference between the two clusters. Additionally, all isolated strains differed phenotypically from V. cholerae in their ability to utilize N-acetyl-d-galactosamine and d-glucuronic acid as sole carbon sources. Furthermore, they were generally unable to infect the slime mould Dictyostelium discoideum, a widespread ability in V. cholerae. Based on these clear phenotypic differences that are not necessarily apparent in standard tests as well as average nucleotide identity and phylogeny of protein-coding genes, we propose the existence of a novel species, Vibrio metoecus sp. nov. with the type strain OP3H(T) ( = LMG 27764(T) = CIP 110643(T)). Due to its close resemblance to V. cholerae and the increasing number of strains isolated over the past several years, we suggest that V. metoecus sp. nov. is a relatively common species of the genus Vibrio, isolates of which have been identified as atypical isolates of V. cholerae in the past. Its isolation from clinical samples also indicates that strains of this species, like V. cholerae, are opportunistic pathogens. © 2014 IUMS.

  10. Differences in Glycoprotein Complex Receptor Binding Site Accessibility Prompt Poor Cross-Reactivity of Neutralizing Antibodies between Closely Related Arenaviruses.

    Science.gov (United States)

    Brouillette, Rachel B; Phillips, Elisabeth K; Ayithan, Natarajan; Maury, Wendy

    2017-04-01

    The glycoprotein complex (GPC) of arenaviruses, composed of stable signal peptide, GP1, and GP2, is the only antigen correlated with antibody-mediated neutralization. However, despite strong cross-reactivity of convalescent antisera between related arenavirus species, weak or no cross-neutralization occurs. Two closely related clade B viruses, Machupo virus (MACV) and Junín virus (JUNV), have nearly identical overall GPC architecture and share a host receptor, transferrin receptor 1 (TfR1). Given structural and functional similarities of the GP1 receptor binding site (RBS) of these viruses and the recent demonstration that the RBS is an important target for neutralizing antibodies, it is not clear how these viruses avoid cross-neutralization. To address this, MACV/JUNV chimeric GPCs were assessed for interaction with a group of α-JUNV GPC monoclonal antibodies (MAbs) and mouse antisera against JUNV or MACV GPC. All six MAbs targeted GP1, with those that neutralized JUNV GPC-pseudovirions competing with each other for RBS binding. However, these MAbs were unable to bind to a chimeric GPC composed of JUNV GP1 containing a small disulfide bonded loop (loop 10) unique to MACV GPC, suggesting that this loop may block MAbs interaction with the GP1 RBS. Consistent with this loop causing interference, mouse anti-JUNV GPC antisera that solely neutralized pseudovirions bearing autologous GP1 provided enhanced neutralization of MACV GPC when this loop was removed. Our studies provide evidence that loop 10, which is unique to MACV GP1, is an important impediment to binding of neutralizing antibodies and contributes to the poor cross-neutralization of α-JUNV antisera against MACV.IMPORTANCE Multiple New World arenaviruses can cause severe disease in humans, and some geographic overlap exists among these viruses. A vaccine that protects against a broad range of New World arenaviruses is desirable for purposes of simplicity, cost, and broad protection against multiple National

  11. Genetic variability and relationship between MT-1 elephant grass and closely related cultivars assessed by SRAP markers

    Indian Academy of Sciences (India)

    Xin-Ming Xie; Feng Zhou; Xiang-Qian Zhang; Ju-Ming Zhang

    2009-12-01

    Genetic variability and relationships among elephant grass cultivars were estimated by the SRAP (sequence-related amplified polymorphism) assay. A total of 60 individuals collected from five cultivars in China were analysed. Sixty-two selected primer combinations generated 1395 bands, with an average of 22.5 per primer combination. The average value of percentage of polymorphic bands (PPB) was 72.8% at species level. The PPB was from 15.2% to 75%, with an average of 39.6% at cultivar level. $H_{POP}$, within-cultivar Shannon’s index was 1.738 at cultivar level; at species level, the Shannon’s index $(H_{SP})$ was 3.880. An assessment of diversity between cultivars $[(H_{SP} −H_{POP})/H_{SP}]$ indicated that most of the diversity (55.2%) was detected among cultivars, and only 44.8% was within cultivars in total genetic variation. According to UPGMA dendrogram, the five cultivars were clustered into three main groups. One group included MT-1 and Mott with a bootstrap support of 100%, another consisted of Huanan and N51 with a bootstrap support of 81%, and last one was only Guimu-1. The results indicate that the MT-1 and Mott have a closest genetic relationship; Huanan and N51 possess a relatively close relationship, and Guimu-1 is the most distinct from the other four cultivars.

  12. Molecular evidence that the spiny mouse (Acomys) is more closely related to gerbils (Gerbillinae) than to true mice (Murinae).

    Science.gov (United States)

    Chevret, P; Denys, C; Jaeger, J J; Michaux, J; Catzeflis, F M

    1993-04-15

    Spiny mice of the genus Acomys traditionally have been classified as members of the Murinae, a subfamily of rodents that also includes rats and mice with which spiny mice share a complex set of morphological characters, including a unique molar pattern. The origin and evolution of this molar pattern, documented by many fossils from Southern Asia, support the hypothesis of the monophyly of Acomys and all other Murinae. This view has been challenged by immunological studies that have suggested that Acomys is as distantly related to mice (Mus) as are other subfamilies (e.g., hamsters: Cricetinae) of the muroid rodents. We present molecular evidence derived from DNA.DNA hybridization data that indicate that the spiny mouse Acomys and two African genera of Murinae, Uranomys and Lophuromys, constitute a monophyletic clade, a view that was recently suggested on the basis of dental characters. However, our DNA.DNA hybridization data also indicate that the spiny mice (Acomys) are more closely related to gerbils (Gerbillinae) than to the true mice and rats (Murinae) with which they have been classified. Because Acomys and the brush-furred mice Uranomys and Lophuromys share no derived morphological characters with the Gerbillinae, their murine morphology must have evolved by convergence, including the molar pattern previously considered to support the monophyly of the Murinae.

  13. DNA sequence conservation between the Bacillus anthracis pXO2 plasmid and genomic sequence from closely related bacteria

    Directory of Open Access Journals (Sweden)

    Sabin Robert

    2002-12-01

    Full Text Available Abstract Background Complete sequencing and annotation of the 96.2 kb Bacillus anthracis plasmid, pXO2, predicted 85 open reading frames (ORFs. Bacillus cereus and Bacillus thuringiensis isolates that ranged in genomic similarity to B. anthracis, as determined by amplified fragment length polymorphism (AFLP analysis, were examined by PCR for the presence of sequences similar to 47 pXO2 ORFs. Results The two most distantly related isolates examined, B. thuringiensis 33679 and B. thuringiensis AWO6, produced the greatest number of ORF sequences similar to pXO2; 10 detected in 33679 and 16 in AWO6. No more than two of the pXO2 ORFs were detected in any one of the remaining isolates. Dot-blot DNA hybridizations between pXO2 ORF fragments and total genomic DNA from AWO6 were consistent with the PCR assay results for this isolate and also revealed nine additional ORFs shared between these two bacteria. Sequences similar to the B. anthracis cap genes or their regulator, acpA, were not detected among any of the examined isolates. Conclusions The presence of pXO2 sequences in the other Bacillus isolates did not correlate with genomic relatedness established by AFLP analysis. The presence of pXO2 ORF sequences in other Bacillus species suggests the possibility that certain pXO2 plasmid gene functions may also be present in other closely related bacteria.

  14. Identification and characterization of two closely related unclassifiable endogenous retroviruses in pythons (Python molurus and Python curtus).

    Science.gov (United States)

    Huder, Jon B; Böni, Jürg; Hatt, Jean-Michel; Soldati, Guido; Lutz, Hans; Schüpbach, Jörg

    2002-08-01

    Boid inclusion body disease (BIBD) is a fatal disorder of boid snakes that is suspected to be caused by a retrovirus. In order to identify this agent, leukocyte cultures (established from Python molurus specimens with symptoms of BIBD or kept together with such diseased animals) were assessed for reverse transcriptase (RT) activity. Virus from cultures exhibiting high RT activity was banded on sucrose density gradients, and the RT peak fraction was subjected to highly efficient procedures for the identification of unknown particle-associated retroviral RNA. A 7-kb full retroviral sequence was identified, cloned, and sequenced. This virus contained intact open reading frames (ORFs) for gag, pro, pol, and env, as well as another ORF of unknown function within pol. Phylogenetic analysis showed that the virus is distantly related to viruses from both the B and D types and the mammalian C type but cannot be classified. It is present as a highly expressed endogenous retrovirus in all P. molurus individuals; a closely related, but much less expressed virus was found in all tested Python curtus individuals. All other boid snakes tested, including Python regius, Python reticulatus, Boa constrictor, Eunectes notaeus, and Morelia spilota, were virus negative, independent of whether they had BIBD or not. Virus isolated from P. molurus could not be transmitted to the peripheral blood mononuclear cells of B. constrictor or P. regius. Thus, there is no indication that this novel virus, which we propose to name python endogenous retrovirus (PyERV), is causally linked with BIBD.

  15. A Novel CD8-Independent High-Avidity Cytotoxic T-Lymphocyte Response Directed against an Epitope in the Phosphoprotein of the Paramyxovirus Simian Virus 5

    Science.gov (United States)

    Gray, Peter M.; Parks, Griffith D.; Alexander-Miller, Martha A.

    2001-01-01

    Adoptive transfer studies have shown that cytotoxic T lymphocytes (CTL) of high avidity, capable of recognizing low levels of peptide-MHC I molecules, are more efficient at reducing viral titers than are low-avidity CTL, thus establishing CTL avidity as a critical parameter for the ability of a CTL to clear virus in vivo. It has been well documented that CTL of high avidity are relatively CD8 independent, whereas low-avidity CTL require CD8 engagement in order to become activated. In this study we have analyzed the antiviral CTL response elicited following infection with the paramyxovirus simian virus 5 (SV5). We have identified the immunodominant and subdominant CTL responses and subsequently assessed the avidity of these responses by their CD8 dependence. This is the first study in which the relationship between immunodominance and CTL avidity has been investigated. The immunodominant response was directed against an epitope present in the viral M protein, and subdominant responses were directed against epitopes present in the P, F, and HN proteins. Similarly to other CTL responses we have analyzed, the immunodominant response and the subdominant F and HN responses were comprised of both high- and low-avidity CTL. However, the subdominant response directed against the epitope present in the P protein is novel, as it is exclusively high avidity. This high-avidity response is independent of both the route of infection and expression by recombinant SV5. A further understanding of the inherent properties of P that elicit only high-avidity CTL may allow for the design of more efficacious vaccine vectors that preferentially elicit high-avidity CTL in vivo. PMID:11581375

  16. Molecular detection of novel Anaplasmataceae closely related to Anaplasma platys and Ehrlichia canis in the dromedary camel (Camelus dromedarius).

    Science.gov (United States)

    Bastos, Armanda D S; Mohammed, Osama B; Bennett, Nigel C; Petevinos, Charalambos; Alagaili, Abdulaziz N

    2015-09-30

    Serological surveys have confirmed Anaplasma marginale and Anaplasma phagocytophilum infections in dromedary camels, but molecular surveys and genetic characterisation of camel-associated Anaplasma species are lacking. In this study, we detected tick-borne Anaplasmataceae in 30 of 100 (30%) healthy dromedary camels screened using a combined 16S rRNA-groEL PCR-sequencing approach. Nucleotide sequencing confirmed Anaplasmataceae genome presence in 28 of the 33 16S rRNA PCR-positive samples, with two additional positive samples, for which 16S rRNA sequence data were ambiguous, being identified by groEL gene characterisation. Phylogenetic analyses of a 1289 nt segment of the 16S rRNA gene confirmed the presence of a unique Ehrlichia lineage and a discrete Anaplasma lineage, comprising three variants, occurring at an overall prevalence of 4% and 26%, respectively. Genetic characterisation of an aligned 559 nt groEL gene region revealed the camel-associated Anaplasma and Ehrlichia lineages to be novel and most closely related to Anaplasma platys and Ehrlichia canis. Based on the confirmed monophyly, minimum pairwise genetic distances between each novel lineage and its closest sister taxon, and the inability to isolate the bacteria, we propose that Candidatus status be assigned to each. This first genetic characterisation of Anaplasmataceae from naturally infected, asymptomatic dromedary camels in Saudi Arabia confirms the presence of two novel lineages that are phylogenetically linked to two pathogenic canid species of increasing zoonotic concern.

  17. The closely related CD103+ dendritic cells (DCs) and lymphoid-resident CD8+ DCs differ in their inflammatory functions.

    Science.gov (United States)

    Jiao, Zhijun; Bedoui, Sammy; Brady, Jamie L; Walter, Anne; Chopin, Michael; Carrington, Emma M; Sutherland, Robyn M; Nutt, Stephen L; Zhang, Yuxia; Ko, Hyun-Ja; Wu, Li; Lew, Andrew M; Zhan, Yifan

    2014-01-01

    Migratory CD103+ and lymphoid-resident CD8+ dendritic cells (DCs) share many attributes, such as dependence on the same transcription factors, cross-presenting ability and expression of certain surface molecules, such that it has been proposed they belong to a common sub-lineage. The functional diversity of the two DC types is nevertheless incompletely understood. Here we reveal that upon skin infection with herpes simplex virus, migratory CD103+ DCs from draining lymph nodes were more potent at inducing Th17 cytokine production by CD4+ T cells than CD8+ DCs. This superior capacity to drive Th17 responses was also evident in CD103+ DCs from uninfected mice. Their differential potency to induce Th17 differentiation was reflected by higher production of IL-1β and IL-6 by CD103+ DCs compared with CD8+ DCs upon stimulation. The two types of DCs from isolated lymph nodes also differ in expression of certain pattern recognition receptors. Furthermore, elevated levels of GM-CSF, typical of those found in inflammation, substantially increased the pool size of CD103+ DCs in lymph nodes and skin. We argue that varied levels of GM-CSF may explain the contrasting reports regarding the positive role of GM-CSF in regulating development of CD103+ DCs. Together, we find that these two developmentally closely-related DC subsets display functional differences and that GM-CSF has differential effect on the two types of DCs.

  18. The Use of Differential EXAFS Analysis for the determination of Small Structural Differences between two closely-related Ruthenium Complexes

    Science.gov (United States)

    Gianolio, D.; Borfecchia, E.; Garino, C.; Ruiu, T.; Lamberti, C.; Salassa, L.

    2013-04-01

    X-ray Absorption Spectroscopy (XAS) is a sensitive and powerful technique in revealing the structure of a material, providing as well high accuracy on interatomic distances. Nevertheless, when dealing with systems that differ only by small structural features, a standard data analysis might be unable of discriminating between such differences. A differential approach was proposed by Bressler, Chergui, and co-workers [2003, Phys. Rev. Lett. 90, 047403][2006, J. Phys. Chem B, 110, 14035][2009 Angew. Chem., Int. Ed. 48 2711] to solve this problem and differentiate between excited and unexcited state structures during pump-and-probe transient XAS experiments. In this contribution, we apply the differential data analysis procedure to the study of two closely-related molecular complexes, namely cis-[Ru(bpy)2(py)2]2+ and cis-[Ru(bpy)2(py)(H2O)]2+, characterized under static conditions. It is herein demonstrated that the method, based on a direct fit of differential curves, is able to reveal the small differences present between the two structures which, conversely, could not be resolved by standard EXAFS fitting of full spectra.

  19. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V.; Dubchak, Inna

    2009-07-23

    The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.

  20. Differences in c-Jun N-terminal kinase recognition and phosphorylation of closely related stathmin-family members.

    Science.gov (United States)

    Yip, Yan Y; Yeap, Yvonne Y C; Bogoyevitch, Marie A; Ng, Dominic C H

    2014-03-28

    The stathmin (STMN) family of tubulin-binding phosphoproteins are critical regulators of interphase microtubule dynamics and organization in a broad range of cellular processes. c-Jun N-terminal kinase (JNK) signalling to STMN family proteins has been implicated specifically in neuronal maturation, degeneration and cell stress responses more broadly. Previously, we characterized mechanisms underlying JNK phosphorylation of STMN at proline-flanked serine residues (Ser25 and Ser38) that are conserved across STMN-like proteins. In this study, we demonstrated using in vitro kinase assays and alanine replacement of serine residues that JNK phosphorylated the STMN-like domain (SLD) of SCG10 on Ser73, consistent with our previous finding that STMN Ser38 was the primary JNK target site. In addition, we confirmed that a JNK binding motif ((41)KKKDLSL(47)) that facilitates JNK targeting of STMN is conserved in SCG10. In contrast, SCLIP was phosphorylated by JNK primarily on Ser60 which corresponds to Ser25 on STMN. Moreover, although the JNK-binding motif identified in STMN and SCG10 was not conserved in SCLIP, JNK phosphorylation of SCLIP was inhibited by a substrate competitive peptide (TI-JIP) highlighting kinase-substrate interaction as required for JNK targeting. Thus, STMN and SCG10 are similarly targeted by JNK but there are clear differences in JNK recognition and phosphorylation of the closely related family member, SCLIP.

  1. Genetic entities and mating system in hermaphroditic Fucus spiralis and its close dioecious relative F. vesiculosus (Fucaceae, Phaeophyceae).

    Science.gov (United States)

    Engel, C R; Daguin, C; Serrão, E A

    2005-06-01

    To date, molecular markers have not settled the question of the specific status of the closely related, but phylogenetically unresolved, brown seaweeds, hermaphroditic Fucus spiralis and dioecious Fucus vesiculosus, nor their propensity for natural hybridization. To test the degree of species integrity and to assess effect of the mating system on the population genetic structure, 288 individuals coming from parapatric (discontinuous) and sympatric (contiguous) spatial configurations at two sites were genotyped with five microsatellite loci. Using a Bayesian admixture analysis, our results show that F. spiralis and F. vesiculosus comprise clearly distinct genetic entities (clusters) generally characterized by cosexual and unisexual individuals, respectively. Genetic diversity within each entity suggests that F. spiralis reproduces primarily through selfing while F. vesiculosus is characterized by an endogamous breeding regime. Nevertheless, aberrant sexual phenotypes were observed in each cluster, no diagnostic alleles were revealed and 10% of study individuals were intermediate between the two genetic entities. This pattern can be explained by recent divergence of two taxa with retention of ancestral polymorphism or asymmetrical, introgressive hybridization. However, given (i) coincident monomorphism at three loci in spiralis clusters and (ii) that significantly more intermediates were observed in sympatric stations than in parapatric stations, we argue that interspecific gene flow has occurred after divergence of the two taxa. Finally, we show that whether recently separated or recently introgressive, the divergent breeding systems probably contribute to species integrity in these two taxa.

  2. Wing pattern morphology of three closely related Melitaea (Lepidoptera, Nymphalidae species reveals highly inaccurate external morphology-based species identification

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    Jure Jugovic

    2014-06-01

    Full Text Available Wing morphology of the three closely related species of Melitaea – M. athalia (Rottemburg, 1775, M. aurelia (Nickerl, 1850 and M. britomartis Assmann, 1847 – co-occurring in the Balkans (SE Europe was investigated in detail through visual inspection, morphometric analysis and multivariate statistical analysis. Results are compared to recent phylogenetic studies, searching for concordant patterns and discrepancies between the two approaches. The morphology of the genitalic structures is also compared with the results of the other two approaches. The main conclusions are as follows: (1 small albeit significant differences in wing morphology exist among the three species and (2 while the structure of male genitalia and phylogenetic position of the three species are concordant, they are (3 in discordance with the wing morphology. The present study represents another example where identification based on external morphology would lead to highly unreliable determinations, hence identification based on phylogenetic studies and/or genitalia is strongly recommended not only for the three studied species but also more broadly within the genus. Furthermore, we show that some of the characters generally used in the identification of these three Melitaea species should be avoided in future.

  3. Identification of structurally closely related monosaccharide and disaccharide isomers by PMP labeling in conjunction with IM-MS/MS.

    Science.gov (United States)

    Yang, Hongmei; Shi, Lei; Zhuang, Xiaoyu; Su, Rui; Wan, Debin; Song, Fengrui; Li, Jinying; Liu, Shuying

    2016-06-16

    It remains particularly difficult for gaining unambiguous information on anomer, linkage, and position isomers of oligosaccharides using conventional mass spectrometry (MS) methods. In our laboratory, an ion mobility (IM) shift strategy was employed to improve confidence in the identification of structurally closely related disaccharide and monosaccharide isomers using IMMS. Higher separation between structural isomers was achieved using 1-phenyl-3-methyl-5-pyrazolone (PMP) derivatization in comparison with phenylhydrazine (PHN) derivatization. Furthermore, the combination of pre-IM fragmentation of PMP derivatives provided sufficient resolution to separate the isomers not resolved in the IMMS. To chart the structural variation observed in IMMS, the collision cross sections (CCSs) for the corresponding ions were measured. We analyzed nine disaccharide and three monosaccharide isomers that differ in composition, linkages, or configuration. Our data show that coexisting carbohydrate isomers can be identified by the PMP labeling technique in conjunction with ion-mobility separation and tandem mass spectrometry. The practical application of this rapid and effective method that requires only small amounts of sample is demonstrated by the successful analysis of water-soluble ginseng extract. This demonstrated the potential of this method to measure a variety of heterogeneous sample mixtures, which may have an important impact on the field of glycomics.

  4. Candida parapsilosis sensu stricto and the closely related species Candida orthopsilosis and Candida metapsilosis in vulvovaginal candidiasis.

    Science.gov (United States)

    Zhu, Yuxia; Shan, Yingying; Fan, Shangrong; Li, Jianling; Liu, Xiaoping

    2015-02-01

    This study aimed to determine the clinical characteristics and in vitro susceptibilities of Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis isolates from patients with vulvovaginal candidiasis (VVC). We analysed 63 vaginal C. parapsilosis specimens. After the molecular analyses, the isolates were characterised as C. parapsilosis sensu stricto (77.8%), C. orthopsilosis (7.9%) and C. metapsilosis (14.3%). The signs and symptoms of VVC caused by C. parapsilosis sensu lato, including itching, erythema and abnormal discharge, were milder than those caused by C. albicans. None of the C. parapsilosis sensu lato isolates were resistant to fluconazole, miconazole or itraconazole. The resistance rates of C. albicans to fluconazole, itraconazole, miconazole and clotrimazole were 2.3, 1.5, 3.1 and 0.8%, respectively. Both C. parapsilosis sensu lato and C. albicans were susceptible to nystatin. The mycological eradication rate at follow-up days 7-14 and 30-35 were 77.8% (49/63) and 76.2% (48/63), respectively, when treated with various antifungal agents and regimens. We conclude that C. parapsilosis sensu stricto and the closely related species C. orthopsilosis and C. metapsilosis were present in the vaginal samples of VVC patients. The symptoms and signs of VVC caused by C. parapsilosis are milder than those caused by C. albicans. The antifungal susceptibility and therapeutic efficacy in patients colonised by C. parapsilosis sensu lato were similar to those observed in C. albicans-colonised patients.

  5. The closely related CD103+ dendritic cells (DCs and lymphoid-resident CD8+ DCs differ in their inflammatory functions.

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    Zhijun Jiao

    Full Text Available Migratory CD103+ and lymphoid-resident CD8+ dendritic cells (DCs share many attributes, such as dependence on the same transcription factors, cross-presenting ability and expression of certain surface molecules, such that it has been proposed they belong to a common sub-lineage. The functional diversity of the two DC types is nevertheless incompletely understood. Here we reveal that upon skin infection with herpes simplex virus, migratory CD103+ DCs from draining lymph nodes were more potent at inducing Th17 cytokine production by CD4+ T cells than CD8+ DCs. This superior capacity to drive Th17 responses was also evident in CD103+ DCs from uninfected mice. Their differential potency to induce Th17 differentiation was reflected by higher production of IL-1β and IL-6 by CD103+ DCs compared with CD8+ DCs upon stimulation. The two types of DCs from isolated lymph nodes also differ in expression of certain pattern recognition receptors. Furthermore, elevated levels of GM-CSF, typical of those found in inflammation, substantially increased the pool size of CD103+ DCs in lymph nodes and skin. We argue that varied levels of GM-CSF may explain the contrasting reports regarding the positive role of GM-CSF in regulating development of CD103+ DCs. Together, we find that these two developmentally closely-related DC subsets display functional differences and that GM-CSF has differential effect on the two types of DCs.

  6. Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.].

    Science.gov (United States)

    Scotti-Saintagne, Caroline; Mariette, Stéphanie; Porth, Ilga; Goicoechea, Pablo G; Barreneche, Teresa; Bodénès, Catherine; Burg, Kornel; Kremer, Antoine

    2004-11-01

    Interspecific differentiation values (G(ST)) between two closely related oak species (Quercus petraea and Q. robur) were compiled across different studies with the aim to explore the distribution of differentiation at the genome level. The study was based on a total set of 389 markers (isozymes, AFLPs, SCARs, microsatellites, and SNPs) for which allelic frequencies were estimated in pairs of populations sampled throughout the sympatric distribution of the two species. The overall distribution of G(ST) values followed an L-shaped curve with most markers exhibiting low species differentiation (G(ST) 10% levels. Twelve percent of the loci exhibited significant G(ST) deviations to neutral expectations, suggesting that selection contributed to species divergence. Coding regions expressed higher differentiation than noncoding regions. Among the 389 markers, 158 could be mapped on the 12 linkage groups of the existing Q. robur genetic map. Outlier loci with large G(ST) values were distributed over 9 linkage groups. One cluster of three outlier loci was found within 0.51 cM; but significant autocorrelation of G(ST) was observed at distances <2 cM. The size and distribution of genomic regions involved in species divergence are discussed in reference to hitchhiking effects and disruptive selection.

  7. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.

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    Thomas Mailund

    Full Text Available We present a hidden Markov model (HMM for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjacent nucleotides in two genomic sequences, such that the nucleotides can be separated by recombination, can migrate between populations, or can coalesce at variable time points, all dependent on the parameters of the model, which are the effective population sizes, splitting times, recombination rate, and migration rate. We show by extensive simulations that the HMM can accurately infer all parameters except the recombination rate, which is biased downwards. Inference is robust to variation in the mutation rate and the recombination rate over the sequence and also robust to unknown phase of genomes unless they are very closely related. We provide a test for whether divergence is gradual or instantaneous, and we apply the model to three key divergence processes in great apes: (a the bonobo and common chimpanzee, (b the eastern and western gorilla, and (c the Sumatran and Bornean orang-utan. We find that the bonobo and chimpanzee appear to have undergone a clear split, whereas the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation.

  8. Spotted fever group rickettsia closely related to Rickettsia monacensis isolated from ticks in South Jeolla province, Korea.

    Science.gov (United States)

    Lee, Kyung-Min; Choi, Yeon-Joo; Shin, Sun-Hye; Choi, Min-Kyung; Song, Hyeon-Je; Kim, Heung-Chul; Klein, Terry A; Richards, Allen L; Park, Kyung-Hee; Jang, Won-Jong

    2013-07-01

    Rickettsia monacensis, a spotted fever group rickettsia, was isolated from Ixodes nipponensis ticks collected from live-captured small mammals in South Jeolla province, Korea in 2006. Homogenates of tick tissues were inoculated into L929 and Vero cell monolayers using shell vial assays. After several passages, Giemsa staining revealed rickettsia-like organisms in the inoculated Vero cells, but not the L929 cells. Sequencing analysis revealed that the ompA-small part (25-614 bp region), ompA-large part (2849-4455 bp region), nearly full-length ompB (58-4889 bp region) and gltA (196-1236 bp region) of the isolates had similarities of 100%, 99.8%, 99.3% and 99.5%, respectively, to those of R. monacensis. Furthermore, phylogenetic analysis showed that the isolate was grouped into the cluster in the same way as R. monacensis in the trees of all genes examined. These results strongly suggest that the isolate is closely related to R. monacensis. As far as is known, this is the first report of isolation of R. monacensis from ticks in Korea.

  9. Frequent cytoplasmic exchanges between oak species that are not closely related: Quercus suber and Q. ilex in Morocco.

    Science.gov (United States)

    Belahbib, N; Pemonge, M H; Ouassou, A; Sbay, H; Kremer, A; Petit, R J

    2001-08-01

    Chloroplast (cp) and mitochondrial (mt) DNA variation were studied in 97 populations of cork oak (Quercus suber) in Morocco; in 31 of these populations, holm oak (Quercus ilex), a clearly distinct species, also occurred and was compared with Q. suber. Three cpDNA and one mtDNA primer pairs were used in the survey, each in combination with one restriction enzyme. Six haplotypes belonging to two very divergent lineages were detected; one lineage predominates in each species, and is probably ancestral, as inferred from comparisons with other oak species. In the mixed-species populations, cytoplasmic genomes were frequently shared across species, as indicated by an introgression ratio of 0.63. This index is a new measure of the propensity of species to share locally genetic markers, varying from zero (complete differentiation) to one (no differentiation). By contrast, more closely related deciduous oak species (Q. robur, Q. petraea and Q. pubescens) have introgression ratios varying from 0.82 to 0.97. The introgression events appear to have been more frequent in the direction Q. ilex (female) x Q. suber (male), a finding which seems attributable to the flowering phenology of these two species. This asymmetry may have favoured immigration of Q. suber beyond its main range, in regions already colonized by Q. ilex. There, rare hybridization and further introgression through long distance pollen flow have established populations that are morphologically indistinguishable from Q. suber but that have cytoplasmic genomes originating from the local Q. ilex populations.

  10. Hybridization between alien species Rumex obtusifolius and closely related native vulnerable species R. longifolius in a mountain tourist destination

    Science.gov (United States)

    Takahashi, Koichi; Hanyu, Masaaki

    2015-01-01

    Alien species expand their distribution by transportation network development. Hybridization between alien species Rumex obtusifolius and closely related native vulnerable species R. longifolius was examined in a mountain tourist destination in central Japan. The three taxa were morphologically identified in the field. Stem height and leaf area were greater in R. longifolius than R. obtusifolius; hybrids were intermediate between the two Rumex species. R. longifolius and the hybrids grew mainly in wet land and the river tributary; R. obtusifolius grew mainly at the roadside and in meadows. Hybrid germination rates of pollen and seeds were much lower than for the two Rumex species. Clustering analysis showed the three taxa each formed a cluster. Most hybrids were F1 generation; the possibility was low of introgression into the two Rumex species by backcross. This study clarified that (1) hybridization occurred between R. obtusifolius and R. longifolius because they occurred together in a small area, but grew in different water habitat conditions, and (2) hybridization was mostly F1 generation because hybrid pollen and seed fertility was low. However, we need caution about introgression into R. longifolius by R. obtusifolius in this area because of the slight possibility of F2 generation and backcrosses. PMID:26354180

  11. Sequence and characterization of six mitochondrial subgenomes from Globodera rostochiensis: multipartite structure is conserved among close nematode relatives.

    Science.gov (United States)

    Gibson, Tracey; Blok, Vivian C; Dowton, Mark

    2007-09-01

    Recently, a multipartite mitochondrial genome was characterized in the potato cyst nematode, Globodera pallida. Six subgenomic circles were detectable by PCR, while full-length genomes were not. We investigate here whether this subgenomic organization occurs in a close relative of G. pallida. We amplified and sequenced one entire mitochondrial subgenome from the cyst-forming nematode, Globodera rostochiensis. Comparison of the noncoding region of this subgenome with those reported previously for G. pallida facilitated the design of amplification primers for a range of subgenomes from G. rostochiensis. We then randomly sequenced five subgenomic fragments, each representative of a unique subgenome. This study indicates that the multipartite structure reported for G. pallida is conserved in G. rostochiensis. A comparison of subgenomic organization between these two Globodera species indicates a considerable degree of overlap between them. Indeed, we identify two subgenomes with an organization identical with that reported for G. pallida. However, other subgenomes are unique to G. rostochiensis, although some of these have blocks of genes comparable to those in G. pallida. Dot-plot comparisons of pairs of subgenomes from G. rostochiensis indicate that the different subgenomes share fragments with high sequence identity. We interpret this as evidence that recombination is operating in the mitochondria of G. rostochiensis.

  12. Hybridization between alien species Rumex obtusifolius and closely related native vulnerable species R. longifolius in a mountain tourist destination.

    Science.gov (United States)

    Takahashi, Koichi; Hanyu, Masaaki

    2015-09-10

    Alien species expand their distribution by transportation network development. Hybridization between alien species Rumex obtusifolius and closely related native vulnerable species R. longifolius was examined in a mountain tourist destination in central Japan. The three taxa were morphologically identified in the field. Stem height and leaf area were greater in R. longifolius than R. obtusifolius; hybrids were intermediate between the two Rumex species. R. longifolius and the hybrids grew mainly in wet land and the river tributary; R. obtusifolius grew mainly at the roadside and in meadows. Hybrid germination rates of pollen and seeds were much lower than for the two Rumex species. Clustering analysis showed the three taxa each formed a cluster. Most hybrids were F1 generation; the possibility was low of introgression into the two Rumex species by backcross. This study clarified that (1) hybridization occurred between R. obtusifolius and R. longifolius because they occurred together in a small area, but grew in different water habitat conditions, and (2) hybridization was mostly F1 generation because hybrid pollen and seed fertility was low. However, we need caution about introgression into R. longifolius by R. obtusifolius in this area because of the slight possibility of F2 generation and backcrosses.

  13. The Dynamics of Genetic Interactions between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment.

    Science.gov (United States)

    Orata, Fabini D; Kirchberger, Paul C; Méheust, Raphaël; Barlow, E Jed; Tarr, Cheryl L; Boucher, Yan

    2015-10-09

    Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the United States. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of 20 V. cholerae and 4 V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as 4 clinical V. metoecus strains were sequenced and compared with reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. Vibrio metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin-coregulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. Vibrio metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment. © The Author(s) 2015. Published by Oxford University Press on behalf of the

  14. Light response, oxidative stress management and nucleic acid stability in closely related Linderniaceae species differing in desiccation tolerance.

    Science.gov (United States)

    Dinakar, Challabathula; Bartels, Dorothea

    2012-08-01

    In the present study, three closely related Linderniaceae species which differ in their sensitivity to desiccation are compared in response to light and oxidative stress defence. Lindernia brevidens, a desiccation-tolerant plant, displayed intense purple pigmentation in leaves under long-day conditions in contrast to Craterostigma plantagineum (desiccation tolerant) and Lindernia subracemosa (desiccation sensitive). The intense pigmentation in leaves does not affect the desiccation tolerance behaviour but seems to be related to oxidative stress protection. Green leaves of short-day and purple leaves of long-day plants provided suitable material for comparing basic photosynthetic parameters. An increase in non-photochemical quenching in purple leaves appears to prevent photoinhibition. Treatment with methyl viologen decreased the photochemical activities in both long-day and short-day plants but long-day plants which accumulate anthocyanins maintained a higher non-photochemical quenching than short-day plants. No differences were seen in the expression of desiccation-induced proteins and proteins involved in carbohydrate metabolism in short-day and long-day grown plants, whereas differences were observed in the expression of transcripts encoding chloroplast-localised stress proteins and transcripts encoding antioxidant enzymes. While the expression of genes encoding antioxidant enzymes were either constitutive or up-regulated during desiccation in C. plantagineum, the expression was down-regulated in L. subracemosa. RNA expression analysis indicated degradation of mRNA during desiccation in L. subracemosa but not in desiccation tolerant species. These results indicate that a better oxidative stress management and mRNA stability are correlated with desiccation tolerance.

  15. Determination of the seroprevalence of Newcastle disease virus (avian paramyxovirus type 1 in Zambian backyard chicken flocks

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    Chimuka Musako

    2012-02-01

    Full Text Available A cross-sectional study was conducted in five provinces and 11 districts of Zambia to determine the seroprevalence of Newcastle disease in Zambian backyard chicken flocks. Of the chickens sampled, 73.9% tested positive for avian paramyxovirus type 1 antibodies by means of an enzyme-linked immunosorbent assay. Seroprevalence varied amongst the five provinces sampled, ranging from 82.6% in the Eastern Province to 48.3% in Luapula Province. Seroprevalence also varied amongst the 11 districts sampled, ranging from 91.3% in Monze district of Southern Province to 22.8% in Mufulira district of the Copperbelt province. Overall, the seroprevalence of Newcastle disease in Zambian backyard chicken flocks has increased since the previous study conducted in 1994.

  16. The Closed End Fund in the Vietnam Stock Market: An Examination of Market relation, Foreign Speculation, and Investor Sentiment

    OpenAIRE

    Nguyen, Thanh Tung,

    2007-01-01

    The Vietnam stock market is a young and small stock market, but it has attracted much attention from the financial public. The Vietnam stock market is also one of the most volatile markets with 2 “bubbles” and 2 recessions within 1 year. Closed end fund is considered as a measure of the sentiment of individual investors (De Long, Shleifer, Summers, and Waldmann (1990)). Closed end fund is one of the shares that we can measure its fundamentals through the Net Asset Value (NAV). The closed end ...

  17. A study on some welfare-related parameters of hDAF transgenic pigs when compared with their conventional close relatives.

    Science.gov (United States)

    Martelli, G; Sardi, L; Stancampiano, L; Govoni, N; Zannoni, A; Nannoni, E; Forni, M; Bacci, M L

    2014-05-01

    Pigs are increasingly used in medical research as transgenic laboratory animals; however, little knowledge is presently available concerning their welfare assessment. The aim of the present study was to investigate some welfare-related parameters of transgenic pigs intended for xenotrasplantation (human decay-accelerating factor (hDAF)) when compared with their conventional (i.e. not transgenic) close relatives (full sibs and half sibs). A total of 14 Large White female transgenic pigs and 10 female non-transgenic (conventional) pigs from four litters were used. All pigs were from the same conventional boar, donor of the semen treated for sperm-mediated gene transfer. During the experiment, BW ranged from 50 to about 80 kg and pigs were weighed at the beginning and at the end of the experiment. Animals were subjected to a set of behavioural tests: a human approach test (HAT), a novel object test (NOT) and an open-door test (ODT). Food preferences were tested through the offer of different foods (banana, apple, carrot, cracker and lemon). During a 4-day period, pigs were diurnally videotaped to study the prevalence of the different behaviours and social interactions (aggressive and non-aggressive interactions). At the end of the trial, cortisol level had been assessed on bristles. No significant differences (P>0.05) were observed between hDAF transgenic and conventional pigs with respect to growth traits, reactivity towards unexpected situations (HAT, NOT, ODT), food preferences, main behavioural traits, social interactions and hair cortisol.

  18. The changes in various hydroxyproline fractions in aortic tissue of rabbits are closely related to the progression of atherosclerosis

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    Alhomida AS

    2010-03-01

    Full Text Available Abstract Background The most important function of collagen and elastin is to induce several mechanical parameters which are known to play a dominant role in governing mechanical properties of the blood vessels. The aortic tissue of rabbit is one of the important sources of collagen and elastin. The effects of high fat diet (HFD on the hydroxyproline (Hyp fractions in serum and aortic tissues of rabbits and collagen content in the aortic tissues of rabbits have not been documented before. The present study was undertaken to investigate the changes in Hyp fractions in serum and aortic tissues of rabbits and collagen content in the aortic tissues of rabbits during the progression of atherosclerosis. The atherosclerotic model used in this study was the New Zealand white rabbit (male; 12 weeks old. Twenty five rabbits were individually caged, and divided into control group (NOR; n = 10 and HFD group (CHO; n = 15. The control group was fed (100 g/day of normal (NOR diet for a period of 15 weeks. The HFD group was fed normal diet supplemented with 1.0% cholesterol plus 1.0% olive oil (100 g/day for the same period of time. Results We found that the TC, LDLC, and TG (mg/dl were significantly (p Conclusions These results suggest that percentage decrease in various Hyp fractions in aortic tissue of HFD rabbits are closely related to percentage decrease of collagen content in aortic tissues of HFD rabbits. These results also suggest that it may be possible to use the changes in various Hyp fractions in aortic tissues of rabbits as an important risk factor during the progression of atherosclerosis.

  19. Choose Your Weaponry: Selective Storage of a Single Toxic Compound, Latrunculin A, by Closely Related Nudibranch Molluscs.

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    Karen L Cheney

    Full Text Available Natural products play an invaluable role as a starting point in the drug discovery process, and plants and animals use many interesting biologically active natural products as a chemical defense mechanism against predators. Among marine organisms, many nudibranch gastropods are known to derive defensive metabolites from the sponges they eat. Here we investigated the putative sequestration of the toxic compound latrunculin A--a 16-membered macrolide that prevents actin polymerization within cellular processes--which has been identified from sponge sources, by five closely related nudibranch molluscs of the genus Chromodoris. Only latrunculin A was present in the rim of the mantle of these species, where storage reservoirs containing secondary metabolites are located, whilst a variety of secondary metabolites were found in their viscera. The species studied thus selectively accumulate latrunculin A in the part of the mantle that is more exposed to potential predators. This study also demonstrates that latrunculin-containing sponges are not their sole food source. Latrunculin A was found to be several times more potent than other compounds present in these species of nudibranchs when tested by in vitro and in vivo toxicity assays. Anti-feedant assays also indicated that latrunculin A was unpalatable to rock pool shrimps, in a dose-dependent manner. These findings led us to propose that this group of nudibranchs has evolved means both to protect themselves from the toxicity of latrunculin A, and to accumulate this compound in the mantle rim for defensive purposes. The precise mechanism by which the nudibranchs sequester such a potent compound from sponges without disrupting their own key physiological processes is unclear, but this work paves the way for future studies in this direction. Finally, the possible occurrence of both visual and chemosensory Müllerian mimicry in the studied species is discussed.

  20. Studies on two closely related species of octocorallians: biochemical and molecular characteristics of the organic matrices of endoskeletal sclerites.

    Science.gov (United States)

    Rahman, M Azizur; Isa, Y; Uehara, T

    2006-01-01

    Two species of alcyonarian corals, Lobophytum crassum and Sinularia polydactyla, are closely related to each other. It is reported that the calcified organic substances in the skeletons of both contain a protein-polysaccharide complex playing a key role in the regulation of biocalcification. However, information on the matrix proteins of endoskeletal sclerite has been lacking. Hence we studied the proteinaceous organic matrices of sclerites for both species, to analyze the sequences and the functional properties of the proteins present. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the preparations showed four bands of proteins with apparent molecular masses of 102, 67, 48, and 37 kDa for L. crassum and seven bands of 109, 83, 70, 63, 41, 30, and 22 kDa for S. polydactyla. A major protein band of about 67 kDa in L. crassum and two bands of proteins of about 70 and 63 kDa in S. polydactyla yielded N-terminal amino acid sequences. Periodic acid-Schiff staining indicated that the 67-kDa protein in L. crassum, and 83- and 63-kDa proteins in S. polydactyla were glycosylated. For detection of calcium binding proteins, a Ca(2+) overlay analysis was conducted in the extract via (45)Ca autoradiography. The 102- and 67-kDa calcium binding proteins in L. crassum, and the 109- and 63-kDa Ca(2+) binding proteins in S. polydactyla were found to be radioactive. An assay for carbonic anhydrase (CA), which is thought to play an important role in the process of calcification, revealed specific activities. Newly derived protein sequences were subjected to standard sequence analysis involving identification of similarities to other proteins in databases. The significantly different protein expressions and compositional analysis of sequences between two species were demonstrated.

  1. Counteraction of tetherin antiviral activity by two closely related SIVs differing by the presence of a Vpu gene.

    Directory of Open Access Journals (Sweden)

    Kristina Nikovics

    Full Text Available In different primate lentiviruses, three proteins (Vpu, Env and Nef have been shown to have anti-tetherin activities. SIVden is a primate lentivirus harbored by a Cercopithecus denti (C. denti whose genome code for a Vpu gene. We have compared the activity of HIV-1 Vpu and of SIVden Vpu on tetherin proteins from humans, from C. denti and from Cercopithecus neglectus (C. neglectus, a monkey species that is naturally infected by SIVdeb, a virus closely related to SIVden but which does not encode a Vpu protein. Here, we demonstrate that SIVden Vpu, is active against C. denti tetherin, but not against human tetherin. Interestingly, C. neglectus tetherin was more sensitive to SIVden Vpu than to HIV-1 Vpu. We also identify residues in the tetherin transmembrane domains that are responsible for the species-specific Vpu effect. Simultaneous mutation (P40L and T45I of human tetherin conferred sensitivity to SIVden Vpu, while abolishing its sensitivity to HIV-1 Vpu. We next analyzed the anti-tetherin activity of the Nef proteins from HIV-1, SIVden and SIVdeb. All three Nef proteins were unable to rescue virus release in the presence of human or C. denti tetherin. Conversely, SIVdeb Nef enhanced virus release in the presence of C. neglectus tetherin, suggesting that SIVdeb relies on Nef in its natural host. Finally, while HIV-1 Vpu not only removed human tetherin from the cell surface but also directed it for degradation, SIVden Vpu only induced the redistribution of both C. denti and C. neglectus tetherins, resulting in a predominantly perinuclear localization.

  2. Anthracnose disease of centipedegrass turf caused by Colletotrichum eremochloae, a new fungal species closely related to Colletotrichum sublineola.

    Science.gov (United States)

    Crouch, Jo Anne; Tomaso-Peterson, Maria

    2012-01-01

    Colletotrichum is a cosmopolitan, anamorphic fungal genus responsible for anthracnose disease in hundreds of plant species worldwide, including members of the Poaceae. Anthracnose disease of the widely planted, non-native, warm-season lawn grass, Eremochloae ophiuroides (centipedegrass), is commonly encountered in the southern United States, but the causal agent has never been identified. We use DNA sequence data from modern cultures and archival fungarium specimens in this study to determine the identity of the fungus responsible for centipedegrass anthracnose disease and provide experimental confirmation of pathogenicity. C. eremochloae sp. nov., a pathogen of centipedegrass, is proposed based on phylogenetic evidence from four sequence markers (Apn2, Apn2/ Mat1, Sod2, ITS). C. eremochloae isolates from centipedegrass shared common morphology and phenotype with C. sublineola, a destructive pathogen of cultivated sorghum and Johnsongrass weeds (Sorghum halepense, S. vulgaris). Molecular phylogenetic analysis identified C. eremochloae and C. sublineola as closely related sister taxa, but genealogical concordance supported their distinction as unique phylogenetic species. Fixed nucleotide differences between C. eremochloae and C. sublineola were observed from collections of these fungi spanning 105 y, including the 1904 lectotype specimen of C. sublineola. C. eremochloae was identified from a fungarium specimen of centipedegrass intercepted at a USA port from a 1923 Chinese shipment; the multilocus sequence from this specimen was identical to modern samples of the fungus. Thus, it appears that the fungus might have migrated to the USA around the same time that centipedegrass first was introduced to the USA in 1916 from China, where the grass is indigenous. The new species C. eremochloae is described and illustrated, along with a description and discussion of C. sublineola based on the lectotype and newly designated epitype.

  3. Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum.

    Science.gov (United States)

    Walkowiak, Sean; Rowland, Owen; Rodrigue, Nicolas; Subramaniam, Rajagopal

    2016-12-09

    The Fusarium graminearum species complex is composed of many distinct fungal species that cause several diseases in economically important crops, including Fusarium Head Blight of wheat. Despite being closely related, these species and individuals within species have distinct phenotypic differences in toxin production and pathogenicity, with some isolates reported as non-pathogenic on certain hosts. In this report, we compare genomes and gene content of six new isolates from the species complex, including the first available genomes of F. asiaticum and F. meridionale, with four other genomes reported in previous studies. A comparison of genome structure and gene content revealed a 93-99% overlap across all ten genomes. We identified more than 700 k base pairs (kb) of single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) within common regions of the genome, which validated the species and genetic populations reported within species. We constructed a non-redundant pan gene list containing 15,297 genes from the ten genomes and among them 1827 genes or 12% were absent in at least one genome. These genes were co-localized in telomeric regions and select regions within chromosomes with a corresponding increase in SNPs and indels. Many are also predicted to encode for proteins involved in secondary metabolism and other functions associated with disease. Genes that were common between isolates contained high levels of nucleotide variation and may be pseudogenes, allelic, or under diversifying selection. The genomic resources we have contributed will be useful for the identification of genes that contribute to the phenotypic variation and niche specialization that have been reported among members of the F. graminearum species complex.

  4. Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives.

    Science.gov (United States)

    Rosenberg, Noah A

    2006-11-01

    The HGDP-CEPH Human Genome Diversity Cell Line Panel is a widely-used resource for studies of human genetic variation. Here, pairs of close relatives that have been included in the panel are identified. Together with information on atypical and duplicated samples, the inferred relative pairs suggest standardized subsets of the panel for use in future population-genetic studies.

  5. Relation between premorbid adjustment, duration of untreated psychosis and close interpersonal trauma in first-episode psychosis

    DEFF Research Database (Denmark)

    Haahr, Ulrik Helt; Larsen, Tor Ketil; Simonsen, Erik

    2016-01-01

    AIM: Interpersonal traumas are highly prevalent in patients with psychotic disorders. Trauma caused by those close to the patient might have a more profound impact than other types of trauma and may influence early life social functioning. The aim is to investigate the associations between...... different types of trauma, in particular close interpersonal traumas experienced before the age of 18, premorbid factors and baseline clinical characteristics in a sample of first-episode psychosis patients. METHODS: A total of 191 patients from the 'TIPS' cohort completed assessment with the Brief Betrayal...... Trauma Survey at their 5 years follow-up interview. RESULTS: Half of the patients reported that they had experienced interpersonal trauma and one-third reported having experienced close interpersonal trauma before the age of 18. Women reported more sexual abuse, physical attacks and emotional...

  6. Natural infections with Pigeon Paramyxovirus-1: Pathologic changes in Eurasian collared-doves (Streptopelia decaocto) and rock pigeons (Columba livia) in the USA: Data

    Science.gov (United States)

    Isidoro-Ayza, Marcos; Lankton, Julia S.; Knowles, Susan N.; Ip, Hon S.; White, C. LeAnn

    2017-01-01

    We reviewed pathological findings and to a lesser extent epidemiological data from 70 free-ranging columbiforms naturally infected with Pigeon paramyxovirus-1 (PPMV-1) from 25 different PPMV-1 mortality events in columbiforms in the USA. In a subset of 17 birds from 10 of the studied outbreaks, we carried out immunohistochemistry targeting PPMV-1 nucleoprotein to determine the tissue distribution of the virus.

  7. A bridge between a lonely soul and the surrounding world: A study on existential consequences of being closely related to a person with aphasia.

    Science.gov (United States)

    Nyström, Maria

    2011-01-01

    This study illuminates existential consequences of being closely related to a person suffering from aphasia. Seventeen close relatives were interviewed and their narratives were interpreted with inspiration from Ricoeur, Levinas, Husserl, Winnicot, and Maurice Merleau-Ponty. The emerging interpretations resulted in four themes that illuminate a life characterized by lost freedom, staying, a new form of relationship, and growing strong together with others. An overarching theme suggests that a life together with an aphasic person means being used as a bridge between the aphasic person and the surrounding world. Moreover, it illuminates that a close relative to a person with aphasia is a person who does not leave, despite a heavy burden of lonely responsibility. It is concluded that community services need to fulfill their responsibility of providing support to informal caregivers as suggested by the Swedish lawmakers.

  8. A bridge between a lonely soul and the surrounding world: A study on existential consequences of being closely related to a person with aphasia

    Science.gov (United States)

    Nyström, Maria

    2011-01-01

    This study illuminates existential consequences of being closely related to a person suffering from aphasia. Seventeen close relatives were interviewed and their narratives were interpreted with inspiration from Ricoeur, Levinas, Husserl, Winnicot, and Maurice Merleau-Ponty. The emerging interpretations resulted in four themes that illuminate a life characterized by lost freedom, staying, a new form of relationship, and growing strong together with others. An overarching theme suggests that a life together with an aphasic person means being used as a bridge between the aphasic person and the surrounding world. Moreover, it illuminates that a close relative to a person with aphasia is a person who does not leave, despite a heavy burden of lonely responsibility. It is concluded that community services need to fulfill their responsibility of providing support to informal caregivers as suggested by the Swedish lawmakers. PMID:22114621

  9. A bridge between a lonely soul and the surrounding world: A study on existential consequences of being closely related to a person with aphasia

    Directory of Open Access Journals (Sweden)

    Maria Nyström

    2011-11-01

    Full Text Available This study illuminates existential consequences of being closely related to a person suffering from aphasia. Seventeen close relatives were interviewed and their narratives were interpreted with inspiration from Ricoeur, Levinas, Husserl, Winnicot, and Maurice Merleau-Ponty. The emerging interpretations resulted in four themes that illuminate a life characterized by lost freedom, staying, a new form of relationship, and growing strong together with others. An overarching theme suggests that a life together with an aphasic person means being used as a bridge between the aphasic person and the surrounding world. Moreover, it illuminates that a close relative to a person with aphasia is a person who does not leave, despite a heavy burden of lonely responsibility. It is concluded that community services need to fulfill their responsibility of providing support to informal caregivers as suggested by the Swedish lawmakers.

  10. Improved rapid amplification of cDNA ends (RACE) for mapping both the 5' and 3' terminal sequences of paramyxovirus genomes.

    Science.gov (United States)

    Li, Zhuo; Yu, Meng; Zhang, Hong; Wang, Hai-Yan; Wang, Lin-Fa

    2005-12-01

    Rapid amplification of cDNA ends (RACE) is a powerful PCR-based technique for determination of RNA terminal sequences. However, most of the RACE methods reported in the literature are developed specifically for the mapping of eukaryotic transcripts with 3' poly-A tail and 5' cap structure. In this study, an improved RACE strategy was developed which allows both 5' and 3' RACE of paramyxovirus genomic RNA using the same set of common molecular biology reagents without having to rely on expensive RACE kits. Mapping of RNA genome terminal sequences is an essential part of characterizing novel paramyxoviruses since these sequences contain important signals for genome replication and transcription, and are important molecular markers for studying virus evolution. The usefulness of this strategy was demonstrated by rapid characterization of both genome ends for a novel paramyxovirus recently isolated from human kidney primary cells. The RACE strategy described in this paper is simple, cost-effective and can be used to map genome ends of any RNA viruses.

  11. The Relative Effects upon High School Students of Inductive and Programmed Instruction in the Close Reading of Poetry.

    Science.gov (United States)

    Weiss, James David

    To examine the effects of inductive and programmed instruction in the close reading of poetry, four control classes of urban 11th graders receiving inductive instruction in poetry were compared with four equivalent experimental classes using programmed textbooks. Both groups were given free response tests on two poems: one poem, included in…

  12. Not equal in the face of habitat change: closely related fishes differ in their ability to use predation-related information in degraded coral.

    Science.gov (United States)

    Ferrari, Maud C O; McCormick, Mark I; Allan, Bridie J M; Chivers, Douglas P

    2017-04-12

    Coral reefs are biodiversity hotpots that are under significant threat due to the degradation and death of hard corals. When obligate coral-dwelling species die, the remaining species must either move or adjust to the altered conditions. Our goal was to investigate the effect of coral degradation on the ability of coral reef fishes to assess their risk of predation using alarm cues from injured conspecifics. Here, we tested the ability of six closely related species of juvenile damselfish (Pomacentridae) to respond to risk cues in both live coral or dead-degraded coral environments. Of those six species, two are exclusively associated with live coral habitats, two are found mostly on dead-degraded coral rubble, while the last two are found in both habitat types. We found that the two live coral associates failed to respond appropriately to the cues in water from degraded habitats. In contrast, the cue response of the two rubble associates was unaffected in the same degraded habitat. Interestingly, we observed a mixed response from the species found in both habitat types, with one species displaying an appropriate cue response while the other did not. Our second experiment suggested that the lack of responses stemmed from deactivation of the alarm cues, rather than the inability of the species to smell. Habitat preference (live coral versus dead coral associates) and phylogeny are good candidates for future work aimed at predicting which species are affected by coral degradation. Our results point towards a surprising level of variation in the ability of congeneric species to fare in altered habitats and hence underscores the difficulty of predicting community change in degraded habitats. © 2017 The Authors.

  13. When the presence of creative coworkers is related to creativity: role of supervisor close monitoring, developmental feedback, and creative personality.

    Science.gov (United States)

    Zhou, Jing

    2003-06-01

    Study 1 was conducted to examine the contribution of the joint condition of supervisor close monitoring and the presence of creative coworkers to employees' creativity. In addition to replicating Study 1's results, Study 2 examined (a) the joint condition of supervisor developmental feedback and presence of creative coworkers and (b) whether creative personality moderated the contributions of the 2 joint conditions. Converging results from the 2 field studies demonstrated that when creative coworkers were present, the less supervisors engaged in close monitoring, the more employees exhibited creativity. Study 2 also found that the contribution of this joint condition was stronger for employees with less creative personalities and that when creative coworkers were present, the more supervisors provided developmental feedback, the more employees exhibited creativity.

  14. BAF Complex Is Closely Related to and Interacts with NF1/CTF and RNA Polymerase Ⅱ in Gene Transcriptional Activation

    Institute of Scientific and Technical Information of China (English)

    Li-Hui ZHAO; Xue-Qing BA; Xiao-Guang WANG; Xiao-Juan ZHU; Li WANG; Xian-Lu ZENG

    2005-01-01

    Brg- or hBrm-associated factor (BAF) complexes, a chromatin-remodeling complex family of mammalian cells, facilitate transcriptional activity by remodeling nucleosome structure. Brg 1 is the core subunit of Brg-associated factor complexes. In the present study, we investigated the spatial relationship between Brg1 and nuclear factor 1 (NF1/CTF) and RNA polymerase Ⅱ (RNAP Ⅱ) upon gene transcriptional activation in vivo by employing immuno-gold labeling. The data showed that Brg1 was closely co-localized with NF1/CTF and RNAP Ⅱ in HeLa cells. Moreover, the co-immunoprecipitation assay further revealed that Brg1 can be isolated together with NF1/CTF and RNAP Ⅱ in the ConA-stimulated, but not the resting,T lymphocyte. The combined results suggested that BAF complexes can interact with NF1/CTF and RNAP Ⅱ, and this interaction is closely dependent on the activation of gene transcription.

  15. Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms

    Science.gov (United States)

    Phytophthora megakarya (Pmeg) and P. palmivora (Ppal) are closely related species causing black pod rot of cacao. While Ppal is a cosmopolitan plant pathogen, cacao is the only known host of importance for Pmeg. Pmeg is more virulent on cacao than Ppal. Therefore, we have sequenced both the Pmeg and...

  16. A Holistic Approach to Taxonomic Evaluation of Two Closely Related Endangered Freshwater Mussel Species, the Oyster Mussel (Epioblasma capsaeformis) and Tan Riffleshell (Epioblasma florentina walkeri) (Bivalvia: Unionidae)

    OpenAIRE

    Jones, Jess Walter

    2004-01-01

    A Holistic Approach to Taxonomic Evaluation of Two Closely Related Endangered Freshwater Mussel Species, the Oyster Mussel (Epioblasma capsaeformis) and Tan Riffleshell (Epioblasma florentina walkeri) (Bivalvia: Unionidae) by Jess W. Jones Richard J. Neves, Chairperson Fisheries and Wildlife Sciences (ABSTRACT) Primers for 10 polymorphic DNA microsatellite loci were developed and characterized for the endangered oyster mussel Epioblasma capsaeformis from the Clinch River, TN. Microsatellite...

  17. Aspergillus waksmanii sp. nov. and Aspergillus marvanovae sp. nov., two closely related species in section Fumigati

    DEFF Research Database (Denmark)

    Hubka, Vit; Peterson, Stephen W.; Frisvad, Jens Christian

    2013-01-01

    Two new and phylogenetically closely related species in Aspergillus section Fumigati are described and illustrated. Homothallic Aspergillus waksmanii sp. nov. was isolated from New Jersey soil (USA) and is represented by the ex-type isolate NRRL 179T (=CCF 4266T=Thom 4138.HS2T=IBT 31900T). Asperg...

  18. Relative humidity effects on water vapour fluxes measured with closed-path eddy-covariance systems with short sampling lines

    DEFF Research Database (Denmark)

    Fratini, Gerardo; Ibrom, Andreas; Arriga, Nicola

    2012-01-01

    and correction method proposed here is deemed applicable to closed-path systems featuring a broad range of sampling lines, and indeed applicable also to passive gases as a special case. The methods described in this paper are incorporated, as processing options, in the free and open-source eddy......, a composite of two existing approaches, for correcting eddy-covariance fluxes. By means of a comparison with parallel open-path measurements, we show that the mixed method leads to an improved estimation of latent heat fluxes, with respect to the method described by Ibrom et al. (2007). The quantification......-covariance software packages ECO2S and EddyPro....

  19. Mass spectrometry of planetary exospheres at high relative velocity: direct comparison of open- and closed source measurements

    Science.gov (United States)

    Meyer, Stefan; Tulej, Marek; Wurz, Peter

    2016-04-01

    The exploration of habitable worlds around the gas giants in the Solar System is of major interest in upcoming planetary missions. Exactly this theme is addressed by the Jupiter Icy Moons Explorer (JUICE) mission of ESA, which will characterise Ganymede, Europa and Callisto as planetary objects and potential habitats [1], [2]. We developed a prototype of the Neutral gas and Ion Mass spectrometer (NIM) of the Particle Environment Package (PEP) for the JUICE mission intended for composition measurements of neutral gas and thermal plasma. NIM/PEP will be used to measure the chemical composition of the exospheres of the icy Jovian moons. Besides direct ion measurement, the NIM instrument is able to measure the inflowing neutral gas in two different modes: in neutral mode the gas enters directly the ion source (open source) and in thermal mode, the gas gets thermally accommodated to wall temperature by several collisions inside an equilibrium sphere before entering the ion source (closed source). We performed measurements with the prototype NIM using a neutral gas beam of 1 up to 5 km/s velocity in the neutral and thermal mode. The current trajectory of JUICE foresees a flyby velocity of 4 km/s at Europa, other flybys are in the range of 1 up to 7 km/s and velocity in Ganymede orbits is around 2 km/s. Different species are used for gas beam, such as noble gases Ne, Ar, Kr as well as molecules like H2, Methane, Ethane, Propane and more complex ones. We will present the results of these measurements with respect to fragmentation and density enhancements in the closed source mode. Furthermore, we will give a direct comparison between open and closed source mode measurements. References: [1] ESA, "JUICE assessment study report (Yellow Book)", ESA/SRE(2011)18, 2012. [2] O. Grasset, M.K. Dougherty, A. Coustenis, E.J. Bunce, C. Erd, D. Titov, M. Blanc, A. Coates, P. Drossart, L.N. Fletcher, H. Hussmann, R. Jaumann, N. Krupp, J.-P. Lebreton, O. Prieto-Ballesteros, P. Tortora, F

  20. Mass spectrometry of planetary exospheres at high relative velocity: direct comparison of open- and closed-source measurements

    Science.gov (United States)

    Meyer, Stefan; Tulej, Marek; Wurz, Peter

    2017-01-01

    The exploration of habitable environments on or inside icy moons around the gas giants in the solar system is of major interest in upcoming planetary missions. Exactly this theme is addressed by the JUpiter ICy moons Explorer (JUICE) mission of ESA, which will characterise Ganymede, Europa and Callisto as planetary objects and potential habitats. We developed a prototype of the Neutral Gas and Ion Mass spectrometer (NIM) of the Particle Environment Package (PEP) for the JUICE mission intended for composition measurements of neutral gas and thermal plasma. NIM/PEP will be used to measure the chemical composition of the exospheres of the icy Jovian moons. Besides direct ion measurement, the NIM instrument is able to measure the inflowing neutral gas in two different modes: in neutral mode, where the gas enters directly the ion source (open source), and in thermal mode, where the gas gets thermally accommodated to the wall temperature by several collisions inside an equilibrium sphere, called antechamber, before entering the ion source (closed source). We performed measurements with the prototype NIM using a neutral gas beam of 1 up to 4.5 km s-1 velocity in the neutral and thermal mode. The current trajectory of JUICE foresees a flyby velocity of 4 km s-1 at Europa; other flybys are in the range of 1 up to 7 km s-1 and orbital velocity in Ganymede orbits is around 2 km s-1. Different species are used for the gas beam, such as noble gases Ne, Ar, Kr as well as molecules like H2, methane, ethane, propane and more complex ones. The NIM prototype was successfully tested under realistic JUICE mission conditions. In addition, we find that the antechamber (closed source) behaves as expected with predictable density enhancement over the specified mass range and within the JUICE mission phase velocities. Furthermore, with the open source and the closed source we measure almost the same composition for noble gases, as well as for molecules, indicating no additional

  1. New avian paramyxoviruses type I strains identified in Africa provide new outcomes for phylogeny reconstruction and genotype classification.

    Directory of Open Access Journals (Sweden)

    Renata Servan de Almeida

    Full Text Available Newcastle disease (ND is one of the most lethal diseases of poultry worldwide. It is caused by an avian paramyxovirus 1 that has high genomic diversity. In the framework of an international surveillance program launched in 2007, several thousand samples from domestic and wild birds in Africa were collected and analyzed. ND viruses (NDV were detected and isolated in apparently healthy fowls and wild birds. However, two thirds of the isolates collected in this study were classified as virulent strains of NDV based on the molecular analysis of the fusion protein and experimental in vivo challenges with two representative isolates. Phylogenetic analysis based on the F and HN genes showed that isolates recovered from poultry in Mali and Ethiopia form new groups, herein proposed as genotypes XIV and sub-genotype VIf with reference to the new nomenclature described by Diel's group. In Madagascar, the circulation of NDV strains of genotype XI, originally reported elsewhere, is also confirmed. Full genome sequencing of five African isolates was generated and an extensive phylogeny reconstruction was carried out based on the nucleotide sequences. The evolutionary distances between groups and the specific amino acid signatures of each cluster allowed us to refine the genotype nomenclature.

  2. Isolation and characterization of avian paramyxovirus type 3b from farmed Namibian ostriches (Struthio camelus f. dom.).

    Science.gov (United States)

    Kaleta, Erhard F; Werner, Ortrud; Hemberger, Yvonne

    2010-01-01

    Meat and skin from farmed ostriches are valuable products for European consumers. The EU regulations require that ostrich products deamed for export need to come from ostriches that are free of antibodies against Newcastle disease virus (avian paramxovirus type 1, aPMV-1). After the detection of antibodies against aPMV-1 in one of five ostrich farms in Namibia, attempts were made to isolate the causative virus. No aPMV-1 but an avian paramyxovirus type 3 (aPMV-3) was isolated from five pharyngeal/cloacal swabs of clinically healthy farmed Namibian ostriches. Subtype determination proved that all isolates are members of the subtype aPMV-3 of psittacine bird origin and were designated as aPMV-3b. In the haemagglutination inhibition test, the aPMV-3b isolates cross-reacted with aPMV-1. This allows the conclusion that the antibodies originally detected in sera of the ostriches are due to the cross-reaction with aPMV-3b, rather than to an infection with aPMV-1.To our knowledge, this is the first description of the occurrence of aPMV-3b in farmed ostriches.

  3. Biological and Phylogenetic Characterization of Pigeon Paramyxovirus Serotype 1 Circulating in Wild North American Pigeons and Doves▿

    Science.gov (United States)

    Kim, L. Mia; King, Daniel J.; Guzman, Hilda; Tesh, Robert B.; da Rosa, Amelia P. A. Travassos; Bueno, Rudy; Dennett, James A.; Afonso, Claudio L.

    2008-01-01

    As part of West Nile virus surveillance programs in Rhode Island and eastern Texas between 2000 and 2007, brain tissue was collected from 5,608 dead birds representing 21 avian orders found in public places or reported by homeowners. Fifteen Newcastle disease virus isolates were recovered only from birds of the order Columbiformes and were positively identified by the USDA-validated real-time reverse transcription-PCR assay targeting the matrix gene and more specifically as pigeon paramyxovirus serotype 1 (PPMV-1) by hemagglutinin inhibition with monoclonal antibodies. Based upon partial genomic sequencing and phylogenetic analysis, the newly isolated viruses represent a distinct sublineage within class II genotype VIb. All of the viruses (15/15) were classified as virulent based upon their fusion cleavage site motif (112RRKKRF117) and intracerebral pathogenicity indices of >0.7 (ranging from 0.98 to1.35); however, these viruses escaped detection by the fusion gene-based real-time PCR test for virulence. Modifications introduced to the probe site of the fusion gene-based assay allowed rapid virulence detection within this distinct sublineage. PMID:18716227

  4. The enigmatic monotypic crab plover Dromas ardeola is closely related to pratincoles and coursers (Aves, Charadriiformes, Glareolidae

    Directory of Open Access Journals (Sweden)

    Sergio L. Pereira

    2010-01-01

    Full Text Available The phylogenetic placement of the monotypic crab plover Dromas ardeola (Aves, Charadriiformes remains controversial. Phylogenetic analysis of anatomical and behavioral traits using phenetic and cladistic methods of tree inference have resulted in conflicting tree topologies, suggesting a close association of Dromas to members of different suborders and lineages within Charadriiformes. Here, we revisited the issue by applying Bayesian and parsimony methods of tree inference to 2,012 anatomical and 5,183 molecular characters to a set of 22 shorebird genera (including Turnix. Our results suggest that Bayesian analysis of anatomical characters does not resolve the phylogenetic relationship of shorebirds with strong statistical support. In contrast, Bayesian and parsimony tree inference from molecular data provided much stronger support for the phylogenetic relationships within shorebirds, and support a sister relationship of Dromas to Glareolidae (pratincoles and coursers, in agreement with previously published DNA-DNA hybridization studies.

  5. a new record of acanthodactylus cantoris (sauria: lacertidae) and its comparison with closely related a.blanfordi in southeastern iran

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    a new record ofacanthodactylus cantoris from sistan and baluchistan in southeastern iran is presented in this paper,and this lizard is found occurring in the coastal area of the persian gulf from govater to chabahar.this species is mainly sympatric with a.blanfordi,and their habits and habitats support their close relationship within the cantoris group.in total,29 specimens ofa.cantoris (n =12) and a.blanfordi (n =17) were compared morphologically using statistical methods.the occurrence of a.cantoris in iran has been questioned for a long time by different herpetologists,and the distribution,ecology and taxonomy of this newly recorded species were investigated and provided in this paper.an updated identification key for the species of acanthodactylus in iran is given.

  6. Closeness and distance in the nurse-patient relation. The relevance of Edith Stein's concept of empathy.

    Science.gov (United States)

    Määttä, Sylvia M

    2006-01-01

    This paper emanates from the concept of empathy as understood by the German philosopher Edith Stein. It begins by highlighting different interpretations of empathy. According to the German philosopher Martin Buber, empathy cannot be achieved as an act of will. In contrast, the psychologist Carl Rogers believes that empathy is identical with dialogue and is the outcome of a cognitive act of active listening. The empathy concept of Edith Stein, philosopher and follower of Edmund Husserl's phenomenology, goes beyond these conflicting views and offers a more complex interpretation, with relevance for both healthcare and nursing education. When studying Stein's three-level model of empathy, a field of tension between perspectives of closeness and distance becomes apparent. The paper concludes by suggesting Stein's model of empathy as a strategy to overcome the tension and meet the demands of empathy.

  7. High-pressure Raman study of two ferroelectric crystals closely related to PbTiO3

    Science.gov (United States)

    Burns, Gerald; Sanjurjo, J. A.; López-Cruz, E.

    1984-12-01

    We report high-pressure Raman measurements of the zone-center phonons in two ferroelectric crystals that closely resemble the ABO3 perovskite crystal PbTiO3. These crystals are (Pb0.22Ba0.78)TiO3, i.e., Ba replacing Pb on the A site, and Pb(Ti0.81Sn0.19)O3, i.e., Sn replacing Ti on the B site. In both cases, at room temperature, we follow the modes and determine Pc, the transition pressure from the ferroelectric tetragonal phase to the cubic phase, to be 4.3 and 9.0 GPa, respectively. By observing the coalescence to the same frequency of the appropriate high-energy A1(TO)+E(TO) pairs of phonons, we determine the second-order character of the phase transitions at Pc. The tendency towards a second-order phase transition seems to be the rule at Pc as long as one makes the measurements at a temperature well below Tc; this is in agreement with theory. Thus, these systems exhibit tricritical points in the (P,T) phase diagram. The soft-E(TO)-phonon frequency (ω0) and damping constant (γ) can be measured to pressures reasonably close to Pc while the mode remains underdamped. These results are discussed in terms of a frequency-independent damping constant for the behavior of ω0 and γ near Pc. In the (Pb,Ba)TiO3 crystal, the hydrostatic pressure increases the intensity of the soft A1(TO) mode making it observable. This seems to happen in general in the perovskites. In the Pb(Ti,Sn)O3 crystal we observe the coupling of the soft E(TO) mode with an extra mode at 59 cm-1; this also has been studied as a function of temperature.

  8. Identifying the Best-Fitting Factor Structure of the Experience of Close Relations - Revised in a Scandinavian Example.

    Directory of Open Access Journals (Sweden)

    Barbara Hoff Esbjørn

    Full Text Available The aim of this study was to enhance the understanding of cultural and sample differences in the assessment of attachment by examining the factor structure of the Experiences in Close Relationships-Revised (ECR-R. The ECR-R is a self-report measure of adult romantic attachment dimensions. The present study used a Danish sample with the purpose of addressing limitations in previous studies, such as the lack of diversity in cultural background, restricted sample characteristics, and poorly fitting structure models. Participants consisted of 253 parents of children between the ages of 7 and 12 years, 53% being mothers. The parents completed the paper version of the questionnaire. Confirmatory Factor Analyses were carried out to determine whether theoretically and empirically established models including one and two factors would also provide adequate fits in a Danish sample. A previous study using the original ECR suggested that Scandinavian samples may best be described using a five-factor solution. Our results indicated that the one- and two-factor models of the ECR-R did not fit the data well. Exploratory Factor Analysis revealed a five-factor model. Our study provides evidence that further investigation is needed to establish which model may provide the best model fit in the Scandinavian countries.

  9. [Closing diastemas].

    Science.gov (United States)

    Vieira, L C; Pereira, J C; Coradazzi, J L; Francischone, C E

    1990-01-01

    The authors describe a clinical case of closing upper central incisives diastema, reconstructiva of a conoid upper lateral and the rechaping of an upper canine to a lateral incisive. The material used was composite resin.

  10. Specific molecular detection of Anaplasma sp. closely related to Anaplasma phagocytophilum in ixodid ticks and cattle in a pastureland in Hokkaido, Japan.

    Science.gov (United States)

    Ybañez, Adrian P; Tagawa, Michihito; Matsumoto, Kotaro; Kishimoto, Toshio; Yokoyama, Naoaki; Inokuma, Hisashi

    2013-01-01

    Recent molecular analyses of the Anaplasma sp. closely related to Anaplasma phagocytophilum (previously believed to be A. phagocytophilum) in Japan have clarified its distinct phylogenetic position. PCR methods relying on 16S rRNA- and P44/MSP2-based primers designed to detect this species have low sensitivity and specificity. In this study, a highly sensitive and specific nested PCR method using newly designed primers based on heat-shock operon gene (groEL) was developed to detect this species. The method was later used in an epidemiological study testing DNA samples from 85 Ixodid ticks (collected by flagging) and 50 cattle from the same pastureland in Nakaosobetsu, Hokkaido, Japan. Results revealed prevalence rates of 2.4% (2 of 85) in ticks and 2% (1 of 50) in cattle. The present study also reported the first molecular detection of the Anaplasma sp. closely related to A. phagocytophilum in Japan in H. douglasii, and established a new reliable PCR method that detects this Anaplasma sp. closely related to A. phagocytophilum in Japan.

  11. Siderophore-mediated iron acquisition in the entomopathogenic bacterium Pseudomonas entomophila L48 and its close relative Pseudomonas putida KT2440.

    Science.gov (United States)

    Matthijs, Sandra; Laus, Georges; Meyer, Jean-Marie; Abbaspour-Tehrani, Kourosch; Schäfer, Mathias; Budzikiewicz, Herbert; Cornelis, Pierre

    2009-12-01

    Pseudomonas entomophila L48 is a recently identified entomopathogenic bacterium which, upon ingestion, kills Drosophila melanogaster, and is closely related to P. putida. The complete genome of this species has been sequenced and therefore a genomic, genetic and structural analysis of the siderophore-mediated iron acquisition was undertaken. P. entomophila produces two siderophores, a structurally new and unique pyoverdine and the secondary siderophore pseudomonine, already described in P. fluorescens species. Structural analysis of the pyoverdine produced by the closely related P. putida KT2440 showed that this strain produces an already characterised pyoverdine, but different from P. entomophila, and no evidence was found for the production of a second siderophore. Growth stimulation assays with heterologous pyoverdines demonstrated that P. entomophila is able to utilize a large variety of structurally distinct pyoverdines produced by other Pseudomonas species. In contrast, P. putida KT2440 is able to utilize only its own pyoverdine and the pyoverdine produced by P. syringae LMG 1247. Our data suggest that although closely related, P. entomophila is a more efficient competitor for iron than P. putida.

  12. Varying importance of cuticular hydrocarbons and iridoids in the species-specific mate recognition pheromones of three closely related Leptopilina species

    Directory of Open Access Journals (Sweden)

    Ingmar eWeiss

    2015-03-01

    Full Text Available Finding a suitable mate for reproduction is one of the most important tasks for almost all animals. In insects this task is often facilitated by pheromone-mediated communication. While insect pheromones in general show enormous chemical diversity, closely related species often use structurally similar compounds in their pheromones. Despite this similarity, pheromones of congeneric species living in sympatry need to be species specific.We investigated the pheromone-mediated mate recognition by males of three closely related species of Leptopilina, a genus of parasitoid wasps that utilize the larvae of Drosophila as hosts. The study species, L. heterotoma, L. boulardi, and L. victoriae, occur sympatrically and have a similar ecology and life history. We have found that mate recognition is species specific in all three species. This species specificity is achieved by a differing importance of cuticular hydrocarbons (CHCs and iridoids in the female mate recognition pheromones. In L. heterotoma the iridoids are of major importance while CHCs play a negligible role. In L. boulardi, however, the CHCs are as important as the iridoids, while in L. victoriae, the CHCs alone elicit a full behavioral response of males.Our results provide novel insights into pheromone evolution in insects by showing that selection on two completely different classes of chemical compounds may generate conditions where compounds from both classes contribute to a varying degree to the chemical communication of closely related species and that this variation also generates the species specificity of the signals.

  13. Characterization of leaf cuticular waxes and cutin monomers of Camelina sativa and closely-related Camelina species

    Science.gov (United States)

    Camelina sativa is an old world crop newly introduced to the semi-arid regions of the Southwestern US. Recently, Camelina gained attention as a biofuel feedstock crop due to its relatively high oil content, polyunsaturated fatty acids, very short growing season with fairly good adaption to marginal ...

  14. The Relationship between Instructor Misbehaviors and Student Antisocial Behavioral Alteration Techniques: The Roles of Instructor Attractiveness, Humor, and Relational Closeness

    Science.gov (United States)

    Claus, Christopher J.; Booth-Butterfield, Melanie; Chory, Rebecca M.

    2012-01-01

    Using rhetorical/relational goal theory as a guiding frame, we examined relationships between instructor misbehaviors (i.e., indolence, incompetence, and offensiveness) and the likelihood of students communicating antisocial behavioral alteration techniques (BATs). More specifically, the study focused on whether students' perceptions of instructor…

  15. The Relationship between Instructor Misbehaviors and Student Antisocial Behavioral Alteration Techniques: The Roles of Instructor Attractiveness, Humor, and Relational Closeness

    Science.gov (United States)

    Claus, Christopher J.; Booth-Butterfield, Melanie; Chory, Rebecca M.

    2012-01-01

    Using rhetorical/relational goal theory as a guiding frame, we examined relationships between instructor misbehaviors (i.e., indolence, incompetence, and offensiveness) and the likelihood of students communicating antisocial behavioral alteration techniques (BATs). More specifically, the study focused on whether students' perceptions of instructor…

  16. Relation between hydraulic properties and plant coverage of the closed-landfill soils in Piacenza (Po Valley, Italy)

    Science.gov (United States)

    Cassinari, C.; Manfredi, P.; Giupponi, L.; Trevisan, M.; Piccini, C.

    2015-02-01

    In this paper the results of a study of soil hydraulic properties and plant coverage of a landfill located in Piacenza (Po Valley, Italy) are presented, together with the attempt to put the hydraulic properties in relation with plant coverage. The measured soil water retention curve was first compared with the output of some pedotransfer functions taken from the literature and then with the output of the same pedotransfer functions applied to a reference soil. The landfill plant coverage was also studied. The relation between soil hydraulic properties and plant coverage showed that the landfill soils have a low water content available for plants and this fact, together with their lack of depth and compacted structure, justifies the presence of a nitrophilous, disturbed-soil vegetation type, dominated by ephemeral annual species (therophytes).

  17. An analysis of psychotropic drug sales. Increasing sales of selective serotonin reuptake inhibitors anre closely related to number of products

    DEFF Research Database (Denmark)

    Nielsen, Margrethe; Gøtzsche, Peter C.

    2011-01-01

    by changes in sales of the benzodiazepines and SSRIs. We found a decline in the sales of benzodiazepines after a peak in 1986, likely due to the recognition that they cause dependence. From a low level in 1992, we found that the sales of SSRIs increased almost linearly by a factor of 18, up to 44 DDD per......BACKGROUND: Prescribing of selective serotonin reuptake inhibitors (SSRIs) has increased dramatically. OBJECTIVE: To compare the sales of benzodiazepines and SSRIs within the primary care sector in Denmark and relate changes in usage to number of indications and products on the market. METHODS: We...

  18. Discovery of a novel insect neuropeptide signaling system closely related to the insect adipokinetic hormone and corazonin hormonal systems

    DEFF Research Database (Denmark)

    Hansen, Karina Kiilerich; Stafflinger, Elisabeth; Schneider, Martina

    2010-01-01

    that are structurally related to the AKHs but represent a different neuropeptide signaling system. We have previously cloned an orphan GPCR from the malaria mosquito Anopheles gambiae that was structurally intermediate between the A. gambiae AKH and corazonin GPCRs. Using functional expression of the receptor in cells...... receptors, this is a prominent example of receptor/ligand co-evolution, probably originating from receptor and ligand gene duplications followed by mutations and evolutionary selection, thereby yielding three independent hormonal systems. The ACP signaling system occurs in the mosquitoes A. gambiae, Aedes...

  19. Replications of Two Closely Related Groups of Jumbo Phages Show Different Level of Dependence on Host-encoded RNA Polymerase

    Science.gov (United States)

    Matsui, Takeru; Yoshikawa, Genki; Mihara, Tomoko; Chatchawankanphanich, Orawan; Kawasaki, Takeru; Nakano, Miyako; Fujie, Makoto; Ogata, Hiroyuki; Yamada, Takashi

    2017-01-01

    Ralstonia solanacearum phages ΦRP12 and ΦRP31 are jumbo phages isolated in Thailand. Here we show that they exhibit similar virion morphology, genome organization and host range. Genome comparisons as well as phylogenetic and proteomic tree analyses support that they belong to the group of ΦKZ-related phages, with their closest relatives being R. solanacearum phages ΦRSL2 and ΦRSF1. Compared with ΦRSL2 and ΦRSF1, ΦRP12 and ΦRP31 possess larger genomes (ca. 280 kbp, 25% larger). The replication of ΦRP12 and ΦRP31 was not affected by rifampicin treatment (20 μg/ml), suggesting that phage-encoded RNAPs function to start and complete the infection cycle of these phages without the need of host-encoded RNAPs. In contrast, ΦRSL2 and ΦRSF1, encoding the same set of RNAPs, did not produce progeny phages in the presence of rifampicin (5 μg/ml). This observation opens the possibility that some ΦRP12/ΦRP31 factors that are absent in ΦRSL2 and ΦRSF1 are involved in their host-independent transcription. PMID:28659872

  20. New insights into the phylogeny and worldwide dispersion of two closely related nematode species, Bursaphelenchus xylophilus and Bursaphelenchus mucronatus.

    Directory of Open Access Journals (Sweden)

    Filipe Pereira

    Full Text Available The pinewood nematode, Bursaphelenchus xylophilus, is one of the greatest threats to coniferous forests worldwide, causing severe ecological damage and economic loss. The biology of B. xylophilus is similar to that of its closest relative, B. mucronatus, as both species share food resources and insect vectors, and have very similar morphological characteristics, although little pathogenicity to conifers has been associated with B. mucronatus. Using both nuclear and mitochondrial DNA markers, we show that B. xylophilus and B. mucronatus form distinct phylogenetic groups with contrasting phylogeographic patterns. B. xylophilus presents lower levels of intraspecific diversity than B. mucronatus, as expected for a species that evolved relatively recently through geographical or reproductive isolation. Genetic diversity was particularly low in recently colonised areas, such as in southwestern Europe. By contrast, B. mucronatus displays high levels of genetic diversity and two well-differentiated clades in both mitochondrial and nuclear DNA phylogenies. The lack of correlation between genetic and geographic distances in B. mucronatus suggests intense gene flow among distant regions, a phenomenon that may have remained unnoticed due to the reduced pathogenicity of the species. Overall, our findings suggest that B. xylophilus and B. mucronatus have different demographic histories despite their morphological resemblance and ecological overlap. These results suggest that Bursaphelenchus species are a valuable model for understanding the dispersion of invasive species and the risks posed to native biodiversity and ecosystems.

  1. Genes coding for intermediate filament proteins closely related to the hagfish "thread keratins (TK)" alpha and gamma also exist in lamprey, teleosts and amphibians.

    Science.gov (United States)

    Schaffeld, Michael; Schultess, Jan

    2006-05-15

    The "thread keratins (TK)" alpha and gamma so far have been considered highly specialized intermediate filament (IF) proteins restricted to hagfish. From lamprey, we now have sequenced five novel IF proteins closely related to TKalpha and TKgamma, respectively. Moreover, we have detected corresponding sequences in EST and genomic databases of teleosts and amphibians. The structure of the TKalpha genes and the positions of their deduced amino acid sequences in a phylogenetic tree clearly support their classification as type II keratins. The genes encoding TKgamma show a structure typical for type III IF proteins, whereas their positions in phylogenetic trees favor a close relationship to the type I keratins. Considering that most keratin-like sequences detected in the lancelet also exhibit a gene structure typical for type III IF proteins, it seems likely that the keratin gene(s) originated from an ancient type III IF protein gene. According to EST analyses, the expression of the thread keratins in teleost fish and amphibians may be particularly restricted to larval stages, which, in conjunction with the observed absence of TKalpha and TKgamma genes in any of the available Amniota databases, indicates a thread keratin function closely related to larval development in an aquatic environment.

  2. Medical dilemmas associated with rehabilitating confiscated houbara bustards (Chlamydotis undulata macqueenii) after avian pox and paramyxovirus type 1 infection.

    Science.gov (United States)

    Bailey, Thomas A; Silvanose, Christudas; Manvell, Ruth; Gough, Richard E; Kinne, Joerg; Combreau, Olivier; Launay, Fred

    2002-07-01

    Projects to rehabilitate confiscated animals must carefully consider the risks of disease when determining whether to release these animals back into the wild or to incorporate them into captive breeding programs. Avipox and paramyxovirus type 1 (PMV-1) infections are important causes of morbidity and mortality during rehabilitation of confiscated houbara bustards (Chlamydotis undulata macqueenii). This paper presents key findings of an intensive health monitoring program (physical condition, hematology, serology, endoscopy, microbiology, and virology) of two flocks of houbara bustards that survived outbreaks of septicemic avipox and PMV-1 respectively. Mortality in each flock from avipox and PMV-1 infections were 47% and 25% respectively, and the clinicopathologic features and management of each outbreak are presented. Avipox and PMV-1 viruses were not isolated from surviving birds monitored monthly for 11 mo after initial infection nor were septicemic or diptheritic avipox and PMV-1 infections detected in the captive breeding collection into which surviving birds were ultimately integrated up to 24 mo later. Adenovirus was isolated from four birds during the study demonstrating that novel disease agents of uncertain pathogenicity may be carried latently and intermittently shed by confiscated birds. This paper demonstrates the risk of importing pathogens with illegally traded houbara bustards and reinforces the need for surveillance programs at rehabilitation centers for these birds. We recommend that confiscated houbara bustards integrated into captive breeding programs be managed separately from captive-bred stock. Other measures should include separate facilities for adult birds and rearing facilities for offspring derived from different stock lines and strict sanitary measures. Additionally, health monitoring of confiscated birds should continue after birds are integrated into captive flocks.

  3. Recent speciation in three closely related sympatric specialists: inferences using multi-locus sequence, post-mating isolation and endosymbiont data.

    Directory of Open Access Journals (Sweden)

    Huai-Jun Xue

    Full Text Available Shifting between unrelated host plants is relatively rare for phytophagous insects, and distinct host specificity may play crucial roles in reproductive isolation. However, the isolation status and the relationship between parental divergence and post-mating isolation among closely related sympatric specialists are still poorly understood. Here, multi-locus sequence were used to estimate the relationship among three host plant-specific closely related flea beetles, Altica cirsicola, A. fragariae and A. viridicyanea (abbreviated as AC, AF and AV respectively. The tree topologies were inconsistent using different gene or different combinations of gene fragments. The relationship of AF+(AC+AV was supported, however, by both gene tree and species tree based on concatenated data. Post-mating reproductive data on the results of crossing these three species are best interpreted in the light of a well established phylogeny. Nuclear-induced but not Wolbachia-induced unidirectional cytoplasmic incompatibility, which was detected in AC-AF and AF-AV but not in AC-AV, may also suggest more close genetic affinity between AC and AV. Prevalence of Wolbachia in these three beetles, and the endosymbiont in most individuals of AV and AC sharing a same wsp haplotype may give another evidence of AF+(AC+AV. Our study also suggested that these three flea beetles diverged in a relative short time (0.94 My, which may be the result of shifting between unrelated host plants and distinct host specificity. Incomplete post-mating isolation while almost complete lineage sorting indicated that effective pre-mating isolation among these three species should have evolved.

  4. Four tropical, closely related fern species belonging to the genus Adiantum L. are genetically distinct as revealed by ISSR fingerprinting.

    Science.gov (United States)

    Korpelainen, Helena; de Britto, John; Doublet, Jérémy; Pravin, Sahaya

    2005-11-01

    The level and pattern of genetic variation was analyzed in four species of the fern genus Adiantum L., A. hispidulum Sw., A. incisum Forrsk., A. raddianum C.Presl, and A. zollingeri Mett. ex Kuhn, originating from South India, using the ISSR fingerprinting method. The populations of Adiantum possessed a considerable level of genetic variation, the diversity indices ranging from 0.284 to 0.464. Only 12% of the ISSR markers found were restricted to one species only, and 54% were detected in all four species. The analysis of molecular variance revealed that 71.1% of variation was present within populations. The proportion of variation detected among species was only 18.5% while the proportion of variation among populations within species equalled 10.4%. Despite the low level of intrageneric differentiation, the discriminant analysis and clustering of genetic distances indicated that the four Adiantum species are genetically distinct. The F(ST) values calculated for the species were low, varying from 0.089 to 0.179. No linkage disequilibrium was detected between the loci. Such low level of differentiation among populations and the presence of linkage equilibrium reflect that the life history of Adiantum ferns apparently involves common or relatively common sexuality, effective wind-dispersal of spores and outcrossing.

  5. Magnetic resonance imaging of blood brain/nerve barrier dysfunction and leukocyte infiltration: closely related or discordant?

    Directory of Open Access Journals (Sweden)

    Gesa eWeise

    2012-12-01

    Full Text Available Unlike other organs the nervous system is secluded from the rest of the organism by the blood brain (BBB or blood nerve barrier (BNB preventing passive influx of fluids from the circulation. Similarly, leukocyte entry to the nervous system is tightly controlled. Breakdown of these barriers and cellular inflammation are hallmarks of inflammatory as well as ischemic neurological diseases and thus represent potential therapeutic targets. The spatiotemporal relationship between BBB/BNB disruption and leukocyte infiltration has been a matter of debate. We here review contrast-enhanced magnetic resonance imaging (MRI as a non-invasive tool to depict barrier dysfunction and its relation to macrophage infiltration in the central and peripheral nervous system under pathological conditions. Novel experimental contrast agents like Gadofluorine M (Gf allow more sensitive assessment of BBB dysfunction than conventional Gadolinium (Gd-DTPA-enhanced MRI. In addition, Gf facilitates visualization of functional and transient alterations of the BBB remote from lesions. Cellular contrast agents such as superparamagnetic iron oxide particles (SPIO and perfluorocarbons (PFC enable assessment of leukocyte (mainly macrophage infiltration by MR technology. Combined use of these MR contrast agents disclosed that leukocytes can enter the nervous system independent from a disturbance of the BBB, and vice versa, a dysfunctional BBB/BNB by itself is not sufficient to attract inflammatory cells from the circulation. We will illustrate these basic imaging findings in animal models of multiple sclerosis (MS, cerebral ischemia and traumatic nerve injury and review corresponding findings in patients.

  6. Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives.

    Science.gov (United States)

    Layton, Daniel J; Kellogg, Elizabeth A

    2014-03-01

    Species limits of the emerging model organism Setaria viridis (tribe Paniceae, subtribe Cenchrinae) are not well defined. It is thought to be related to S. adhaerens, S. faberi, S. verticillata, and S. verticilliformis and in North America occurs with the morphologically similar S. pumila. An integrated approach was taken to evaluate its variation and relationships with the other taxa. Statistical morphology, flow cytometry, molecular phylogenetics, and growth experiments were employed to examine the group's physical variation, polyploidy, evolutionary relationships, and drought ecology, respectively. SETARIA VIRIDIS contributed one genome to the tetraploids S. faberi, S. verticillata, and S. verticilliformis; the other genome of the latter two was contributed by S. adhaerens. Setaria pumila is unrelated. Morphologically, S. viridis is most similar to S. faberi, but all tested accessions of S. viridis were diploid, whereas those of S. faberi were all tetraploid. Principal component analysis of 70 morphological characters consistently separated S. viridis from S. faberi, largely by spikelet characters. The diagnostic morphological characters are not affected by watering. Setaria faberi is far more sensitive to drought, in terms of mortality and morphological stunting, than S. viridis or S. pumila. SETARIA VIRIDIS is a diploid species and has contributed to several polyploid derivatives. The most morphologically similar of the polyploids is S. faberi, which differs in spikelet features, phylogenetics, genome size, and ecological response to drought. Researchers using field-collected S. viridis as a model organism will benefit from the clear delimitation provided in this study.

  7. Selaginella moellendorffii has a reduced and highly conserved expansin superfamily with genes more closely related to angiosperms than to bryophytes.

    Science.gov (United States)

    Carey, Robert E; Hepler, Nathan K; Cosgrove, Daniel J

    2013-01-03

    Expansins are plant cell wall loosening proteins encoded by a large superfamily of genes, consisting of four families named EXPA, EXPB, EXLA, and EXLB. The evolution of the expansin superfamily is well understood in angiosperms, thanks to synteny-based evolutionary studies of the gene superfamily in Arabidopsis, rice, and Populus. Analysis of the expansin superfamily in the moss Physcomitrella patens revealed a superfamily without EXLA or EXLB genes that has evolved considerably and independently of angiosperm expansins. The sequencing of the Selaginella moellendorffii genome has allowed us to extend these analyses into an early diverging vascular plant. The expansin superfamily in Selaginella moellendorffii has now been assembled from genomic scaffolds. A smaller (and less diverse) superfamily is revealed, consistent with studies of other gene families in Selaginella. Selaginella has an expansin superfamily, which, like Physcomitrella, lacks EXLA or EXLB genes, but does contain two EXPA genes that are related to a particular Arabidopsis-rice clade involved in root hair development. From sequence-based phylogenetic analysis, most Selaginella expansins lie outside the Arabidopsis-rice clades, leading us to estimate the minimum number of expansins present in the last common ancestor of Selaginella and angiosperms at 2 EXPA genes and 1 EXPB gene. These results confirm Selaginella as an important intermediary between bryophytes and angiosperms.

  8. Similar local, but different systemic, metabolomics responses of closely related pine subspecies to folivory by caterpillars of the processionary moth

    Energy Technology Data Exchange (ETDEWEB)

    Rivas-Ubach, A. [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA USA; CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès, Catalonia Spain; Cerdanyola del Vallès, CREAF, Catalonia Spain; Sardans, J. [CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès, Catalonia Spain; Cerdanyola del Vallès, CREAF, Catalonia Spain; Hódar, J. A. [Grupo de Ecología Terrestre, Departamento de Biología Animal y Ecología, Facultad de Ciencias, Universidad de Granada, Granada Spain; Garcia-Porta, J. [Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona Spain; Guenther, A. [Department of Earth System Science, University of California, Irvine CA USA; Global Change Research Centre, Academy of Sciences of the Czech Republic, Brno Czech Republic; Oravec, M. [Global Change Research Centre, Academy of Sciences of the Czech Republic, Brno Czech Republic; Urban, O. [Global Change Research Centre, Academy of Sciences of the Czech Republic, Brno Czech Republic; Peñuelas, J. [CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès, Catalonia Spain; Cerdanyola del Vallès, CREAF, Catalonia Spain; Leiss, K.

    2016-05-16

    Plants respond locally and systemically to herbivore attack. Most of the research conducted on plant-herbivore relationships at elemental and molecular levels have focused on nutrients or/and certain molecular compounds or specific families of defensive metabolites showing that herbivores tend to select plant individuals or species with higher nutrient concentrations and to avoid those with higher levels of phenolics and terpenes. Unfortunately, the defensive role of phenolics in conifers is still unclear. We performed stoichiometric and metabolomics, local and systemic, analyses in two subspecies of Pinus sylvestris under the herbivorous attack by the caterpillars of the pine processionary moth, an important pest in the Mediterranean Basin. Herbivorous attack was not associated with any of the elements analyzed. Both pine subspecies responded locally to folivory mainly by increasing the concentrations of various terpenes and phenolics. Systemic responses differed between subspecies and most of the metabolites presented intermediate concentrations between those of the affected parts and unattacked trees. Contrary as usually thought, foliar nutrient concentrations did not show to be a main factor of an alleged plant selection by adult female processionary moths for oviposition. Local increases in phenolics were more associated with antioxidant function for protection against oxidative damage produced by folivory. On the other hand, terpenes were directly related to defense against herbivores. Herbivory attack produced a general systemic shift in pines, including both primary and secondary metabolisms, that was, however, less intense and chemically different from the local responses. Subspecies responded similarly locally but differently to folivory at systemic level.

  9. Magnetic resonance imaging of blood brain/nerve barrier dysfunction and leukocyte infiltration: closely related or discordant?

    Science.gov (United States)

    Weise, Gesa; Stoll, Guido

    2012-01-01

    Unlike other organs the nervous system is secluded from the rest of the organism by the blood brain barrier (BBB) or blood nerve barrier (BNB) preventing passive influx of fluids from the circulation. Similarly, leukocyte entry to the nervous system is tightly controlled. Breakdown of these barriers and cellular inflammation are hallmarks of inflammatory as well as ischemic neurological diseases and thus represent potential therapeutic targets. The spatiotemporal relationship between BBB/BNB disruption and leukocyte infiltration has been a matter of debate. We here review contrast-enhanced magnetic resonance imaging (MRI) as a non-invasive tool to depict barrier dysfunction and its relation to macrophage infiltration in the central and peripheral nervous system under pathological conditions. Novel experimental contrast agents like Gadofluorine M (Gf) allow more sensitive assessment of BBB dysfunction than conventional Gadolinium (Gd)-DTPA enhanced MRI. In addition, Gf facilitates visualization of functional and transient alterations of the BBB remote from lesions. Cellular contrast agents such as superparamagnetic iron oxide particles (SPIO) and perfluorocarbons enable assessment of leukocyte (mainly macrophage) infiltration by MR technology. Combined use of these MR contrast agents disclosed that leukocytes can enter the nervous system independent from a disturbance of the BBB, and vice versa, a dysfunctional BBB/BNB by itself is not sufficient to attract inflammatory cells from the circulation. We will illustrate these basic imaging findings in animal models of multiple sclerosis, cerebral ischemia, and traumatic nerve injury and review corresponding findings in patients.

  10. Field and experimental evidence of a new caiman trypanosome species closely phylogenetically related to fish trypanosomes and transmitted by leeches

    Directory of Open Access Journals (Sweden)

    Bruno R. Fermino

    2015-12-01

    Full Text Available Trypanosoma terena and Trypanosoma ralphi are known species of the South American crocodilians Caiman crocodilus, Caiman yacare and Melanosuchus niger and are phylogenetically related to the tsetse-transmitted Trypanosoma grayi of the African Crocodylus niloticus. These trypanosomes form the Crocodilian clade of the terrestrial clade of the genus Trypanosoma. A PCR-survey for trypanosomes in caiman blood samples and in leeches taken from caimans revealed unknown trypanosome diversity and frequent mixed infections. Phylogenies based on SSU (small subunit of rRNA and gGAPDH (glycosomal Glyceraldehyde Phosphate Dehydrogenase gene sequences revealed a new trypanosome species clustering with T. terena and T. ralphi in the crocodilian clade and an additional new species nesting in the distant Aquatic clade of trypanosomes, which is herein named Trypanosoma clandestinus n. sp. This new species was found in Caiman yacare, Caiman crocodilus and M. niger from the Pantanal and Amazonian biomes in Brazil. Large numbers of dividing epimastigotes and unique thin and long trypomastigotes were found in the guts of leeches (Haementeria sp. removed from the mouths of caimans. The trypanosomes recovered from the leeches had sequences identical to those of T. clandestinus of caiman blood samples. Experimental infestation of young caimans (Caiman yacare with infected leeches resulted in long-lasting T. clandestinus infections that permitted us to delineate its life cycle. In contrast to T. terena, T. ralphi and T. grayi, which are detectable by hemoculturing, microscopy and standard PCR of caiman blood, T. clandestinus passes undetected by these methods due to very low parasitemia and could be detected solely by the more sensitive nested PCR method. T. clandestinus n. sp. is the first crocodilian trypanosome known to be transmitted by leeches and positioned in the aquatic clade closest to fish trypanosomes. Our data show that caimans can host trypanosomes

  11. Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae).

    Science.gov (United States)

    Wang, Fan-Hong; Lu, Jin-Mei; Wen, Jun; Ebihara, Atsushi; Li, De-Zhu

    2016-01-01

    DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure.

  12. Mimetic Muscles in a Despotic Macaque (Macaca mulatta) Differ from Those in a Closely Related Tolerant Macaque (M. nigra).

    Science.gov (United States)

    Burrows, Anne M; Waller, Bridget M; Micheletta, Jérôme

    2016-10-01

    Facial displays (or expressions) are a primary means of visual communication among conspecifics in many mammalian orders. Macaques are an ideal model among primates for investigating the co-evolution of facial musculature, facial displays, and social group size/behavior under the umbrella of "ecomorphology". While all macaque species share some social behaviors, dietary, and ecological parameters, they display a range of social dominance styles from despotic to tolerant. A previous study found a larger repertoire of facial displays in tolerant macaque species relative to despotic species. The present study was designed to further explore this finding by comparing the gross morphological features of mimetic muscles between the Sulawesi macaque (Macaca nigra), a tolerant species, and the rhesus macaque (M. mulatta), a despotic species. Five adult M. nigra heads were dissected and mimetic musculature was compared to those from M. mulatta. Results showed that there was general similarity in muscle presence/absence between the species as well as muscle form except for musculature around the external ear. M. mulatta had more musculature around the external ear than M. nigra. In addition, M. nigra lacked a zygomaticus minor while M. mulatta is reported to have one. These morphological differences match behavioral observations documenting a limited range of ear movements used by M. nigra during facial displays. Future studies focusing on a wider phylogenetic range of macaques with varying dominance styles may further elucidate the roles of phylogeny, ecology, and social variables in the evolution of mimetic muscles within Macaca Anat Rec, 299:1317-1324, 2016. © 2016 Wiley Periodicals, Inc.

  13. Field and experimental evidence of a new caiman trypanosome species closely phylogenetically related to fish trypanosomes and transmitted by leeches

    Science.gov (United States)

    Fermino, Bruno R.; Paiva, Fernando; Soares, Priscilla; Tavares, Luiz Eduardo R.; Viola, Laerte B.; Ferreira, Robson C.; Botero-Arias, Robinson; de-Paula, Cátia D.; Campaner, Marta; Takata, Carmen S.A.; Teixeira, Marta M.G.; Camargo, Erney P.

    2015-01-01

    Trypanosoma terena and Trypanosoma ralphi are known species of the South American crocodilians Caiman crocodilus, Caiman yacare and Melanosuchus niger and are phylogenetically related to the tsetse-transmitted Trypanosoma grayi of the African Crocodylus niloticus. These trypanosomes form the Crocodilian clade of the terrestrial clade of the genus Trypanosoma. A PCR-survey for trypanosomes in caiman blood samples and in leeches taken from caimans revealed unknown trypanosome diversity and frequent mixed infections. Phylogenies based on SSU (small subunit) of rRNA and gGAPDH (glycosomal Glyceraldehyde Phosphate Dehydrogenase) gene sequences revealed a new trypanosome species clustering with T. terena and T. ralphi in the crocodilian clade and an additional new species nesting in the distant Aquatic clade of trypanosomes, which is herein named Trypanosoma clandestinus n. sp. This new species was found in Caiman yacare, Caiman crocodilus and M. niger from the Pantanal and Amazonian biomes in Brazil. Large numbers of dividing epimastigotes and unique thin and long trypomastigotes were found in the guts of leeches (Haementeria sp.) removed from the mouths of caimans. The trypanosomes recovered from the leeches had sequences identical to those of T. clandestinus of caiman blood samples. Experimental infestation of young caimans (Caiman yacare) with infected leeches resulted in long-lasting T. clandestinus infections that permitted us to delineate its life cycle. In contrast to T. terena, T. ralphi and T. grayi, which are detectable by hemoculturing, microscopy and standard PCR of caiman blood, T. clandestinus passes undetected by these methods due to very low parasitemia and could be detected solely by the more sensitive nested PCR method. T. clandestinus n. sp. is the first crocodilian trypanosome known to be transmitted by leeches and positioned in the aquatic clade closest to fish trypanosomes. Our data show that caimans can host trypanosomes of the aquatic or

  14. Bacillus tequilensis sp. nov., isolated from a 2000-year-old Mexican shaft-tomb, is closely related to Bacillus subtilis.

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    Gatson, Joshua W; Benz, Bruce F; Chandrasekaran, Chitra; Satomi, Masataka; Venkateswaran, Kasthuri; Hart, Mark E

    2006-07-01

    A Gram-positive, spore-forming bacillus was isolated from a sample taken from an approximately 2000-year-old shaft-tomb located in the Mexican state of Jalisco, near the city of Tequila. Tentative identification using conventional biochemical analysis consistently identified the isolate as Bacillus subtilis. DNA isolated from the tomb isolate, strain 10b(T), and closely related species was used to amplify a Bacillus-specific portion of the highly conserved 16S rRNA gene and an internal region of the superoxide dismutase gene (sodA(int)). Trees derived from maximum-likelihood methods applied to the sodA(int) sequences yielded non-zero branch lengths between strain 10b(T) and its closest relative, whereas a comparison of a Bacillus-specific 546 bp amplicon of the 16S rRNA gene demonstrated 99 % similarity with B. subtilis. Although the 16S rRNA gene sequences of strain 10b(T) and B. subtilis were 99 % similar, PFGE of NotI-digested DNA of strain 10b(T) revealed a restriction profile that was considerably different from those of B. subtilis and other closely related species. Whereas qualitative differences in whole-cell fatty acids were not observed, significant quantitative differences were found to exist between strain 10b(T) and each of the other closely related Bacillus species examined. In addition, DNA-DNA hybridization studies demonstrated that strain 10b(T) had a relatedness value of less than 70 % with B. subtilis and other closely related species. Evidence from the sodA(int) sequences, whole-cell fatty acid profiles and PFGE analysis, together with results from DNA-DNA hybridization studies, justify the classification of strain 10b(T) as representing a distinct species, for which the name Bacillus tequilensis sp. nov. is proposed. The type strain is 10b(T) (=ATCC BAA-819(T)=NCTC 13306(T)).

  15. Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithm.

    Science.gov (United States)

    Yang, Cheng-Hong; Chang, Hsueh-Wei; Ho, Chang-Hsuan; Chou, Yii-Cheng; Chuang, Li-Yeh

    2011-03-18

    Complete mitochondrial (mt) genome sequencing is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. For long template sequencing, i.e., like the entire mtDNA, it is essential to design primers for Polymerase Chain Reaction (PCR) amplicons which are partly overlapping each other. The presented chromosome walking strategy provides the overlapping design to solve the problem for unreliable sequencing data at the 5' end and provides the effective sequencing. However, current algorithms and tools are mostly focused on the primer design for a local region in the genomic sequence. Accordingly, it is still challenging to provide the primer sets for the entire mtDNA. The purpose of this study is to develop an integrated primer design algorithm for entire mt genome in general, and for the common primer sets for closely-related species in particular. We introduce ClustalW to generate the multiple sequence alignment needed to find the conserved sequences in closely-related species. These conserved sequences are suitable for designing the common primers for the entire mtDNA. Using a heuristic algorithm particle swarm optimization (PSO), all the designed primers were computationally validated to fit the common primer design constraints, such as the melting temperature, primer length and GC content, PCR product length, secondary structure, specificity, and terminal limitation. The overlap requirement for PCR amplicons in the entire mtDNA is satisfied by defining the overlapping region with the sliding window technology. Finally, primer sets were designed within the overlapping region. The primer sets for the entire mtDNA sequences were successfully demonstrated in the example of two closely-related fish species. The pseudo code for the primer design algorithm is provided. In conclusion, it can be said that our proposed sliding window-based PSO algorithm provides the necessary primer sets for the entire mt genome amplification and

  16. Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithm.

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    Cheng-Hong Yang

    Full Text Available BACKGROUND: Complete mitochondrial (mt genome sequencing is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. For long template sequencing, i.e., like the entire mtDNA, it is essential to design primers for Polymerase Chain Reaction (PCR amplicons which are partly overlapping each other. The presented chromosome walking strategy provides the overlapping design to solve the problem for unreliable sequencing data at the 5' end and provides the effective sequencing. However, current algorithms and tools are mostly focused on the primer design for a local region in the genomic sequence. Accordingly, it is still challenging to provide the primer sets for the entire mtDNA. METHODOLOGY/PRINCIPAL FINDINGS: The purpose of this study is to develop an integrated primer design algorithm for entire mt genome in general, and for the common primer sets for closely-related species in particular. We introduce ClustalW to generate the multiple sequence alignment needed to find the conserved sequences in closely-related species. These conserved sequences are suitable for designing the common primers for the entire mtDNA. Using a heuristic algorithm particle swarm optimization (PSO, all the designed primers were computationally validated to fit the common primer design constraints, such as the melting temperature, primer length and GC content, PCR product length, secondary structure, specificity, and terminal limitation. The overlap requirement for PCR amplicons in the entire mtDNA is satisfied by defining the overlapping region with the sliding window technology. Finally, primer sets were designed within the overlapping region. The primer sets for the entire mtDNA sequences were successfully demonstrated in the example of two closely-related fish species. The pseudo code for the primer design algorithm is provided. CONCLUSIONS/SIGNIFICANCE: In conclusion, it can be said that our proposed sliding window-based PSO

  17. Recommendations on selecting the closing relations for calculating friction pressure drop in the loops of nuclear power stations equipped with VVER reactors

    Science.gov (United States)

    Alipchenkov, V. M.; Belikov, V. V.; Davydov, A. V.; Emel'yanov, D. A.; Mosunova, N. A.

    2013-05-01

    Closing relations describing friction pressure drop during the motion of two-phase flows that are widely applied in thermal-hydraulic codes and in calculations of the parameters characterizing the flow of water coolant in the loops of reactor installations used at nuclear power stations and in other thermal power systems are reviewed. A new formula developed by the authors of this paper is proposed. The above-mentioned relations are implemented in the HYDRA-IBRAE thermal-hydraulic computation code developed at the Nuclear Safety Institute of the Russian Academy of Sciences. A series of verification calculations is carried out for a wide range of pressures, flowrates, and heat fluxes typical for transient and emergency operating conditions of nuclear power stations equipped with VVER reactors. Advantages and shortcomings of different closing relations are revealed, and recommendations for using them in carrying out thermal-hydraulic calculations of coolant flow in the loops of VVER-based nuclear power stations are given.

  18. Natural infections with pigeon paramyxovirus serotype 1: Pathologic changes in Eurasian collared-doves (Streptopelia decaocto) and rock pigeons (Columba livia) in the United States

    Science.gov (United States)

    Isidoro Ayza, Marcos; Afonso, C.L.; Stanton, J.B.; Knowles, Susan N.; Ip, Hon S.; White, C. LeAnn; Fenton, Heather; Ruder, M.G.; Dolinski, A. C.; Lankton, Julia S.

    2017-01-01

    Pigeon paramyxovirus serotype 1 (PPMV-1) is a globally distributed, virulent member of the avian paramyxovirus serotype 1 serogroup that causes mortality in columbiformes and poultry. Following introduction into the United States in the mid-1980s, PPMV-1 rapidly spread causing numerous mortality events in Eurasian collared-doves (Streptopelia decaocto) (ECDOs) and rock pigeons (Columba livia) (ROPIs). The investigators reviewed pathological findings of 70 naturally infected, free-ranging columbiforms from 25 different mortality events in the United States. Immunohistochemistry targeting PPMV-1 nucleoprotein was used to determine the tissue distribution of the virus in a subset of 17 birds from 10 of the studied outbreaks. ECDOs (61 birds) and ROPIs (9 birds) were the only species in which PPMV-1-associated disease was confirmed by viral isolation and presence of histologic lesions. Acute to subacute tubulointerstitial nephritis and necrotizing pancreatitis were the most frequent histologic lesions, with immunolabeling of viral antigen in renal tubular epithelial cells and pancreatic acinar epithelium. Lymphoid depletion of bursa of Fabricius and spleen was common, but the presence of viral antigen in these organs was inconsistent among infected birds. Hepatocellular necrosis was occasionally present with immunolabeling of hypertrophic Kupffer cells, and immunopositive eosinophilic intracytoplasmic inclusion bodies were present in hepatocytes of 1 ECDO. Immunopositive lymphocytic choroiditis was present in 1 ECDO, while lymphocytic meningoencephalitis was frequent in ROPIs in absence of immunolabeling. This study demonstrates widespread presence of PPMV-1 antigen in association with histologic lesions, confirming the lethal potential of this virus in these particular bird species.

  19. Temperature as an ecological factor in the distribution of two closely related freshwater Triclads: an experimental study. [Polycelis tenuis, polycelis nigra

    Energy Technology Data Exchange (ETDEWEB)

    Lascombe, C.; Pattee, E.; Bornard, C.

    1975-01-01

    The influence of temperature on the ecophysiology of two closely related limnophilic Triclads, Polycelis tenuis and P. nigra, in the Lyons region was investigated. Both species have the same physiological rate in the middle zone of the temperature range, but P. tenuis prevails at both ends of the range. It tolerates higher temperatures and its reproduction rate is greater in the cold. Also, because of the existence of physiological races, it seems adapted to a greater diversity of situations. It appears as a real eurytherm. These different points contribute to the explanation of the habitat of both species in the region.

  20. Genomics of sponge-associated Streptomyces spp. closely related to Streptomyces albus J1074: insights into marine adaptation and secondary metabolite biosynthesis potential.

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    Elena Ian

    Full Text Available A total of 74 actinomycete isolates were cultivated from two marine sponges, Geodia barretti and Phakellia ventilabrum collected at the same spot at the bottom of the Trondheim fjord (Norway. Phylogenetic analyses of sponge-associated actinomycetes based on the 16S rRNA gene sequences demonstrated the presence of species belonging to the genera Streptomyces, Nocardiopsis, Rhodococcus, Pseudonocardia and Micromonospora. Most isolates required sea water for growth, suggesting them being adapted to the marine environment. Phylogenetic analysis of Streptomyces spp. revealed two isolates that originated from different sponges and had 99.7% identity in their 16S rRNA gene sequences, indicating that they represent very closely related strains. Sequencing, annotation, and analyses of the genomes of these Streptomyces isolates demonstrated that they are sister organisms closely related to terrestrial Streptomyces albus J1074. Unlike S. albus J1074, the two sponge streptomycetes grew and differentiated faster on the medium containing sea water. Comparative genomics revealed several genes presumably responsible for partial marine adaptation of these isolates. Genome mining targeted to secondary metabolite biosynthesis gene clusters identified several of those, which were not present in S. albus J1074, and likely to have been retained from a common ancestor, or acquired from other actinomycetes. Certain genes and gene clusters were shown to be differentially acquired or lost, supporting the hypothesis of divergent evolution of the two Streptomyces species in different sponge hosts.

  1. Use of two novel approaches to discriminate between closely related host microRNAs that are manipulated by Toxoplasma gondii during infection.

    Science.gov (United States)

    Zeiner, Gusti M; Boothroyd, John C

    2010-06-01

    MicroRNAs (miRNAs) are a class of small, endogenously encoded regulatory RNAs that function to post-transcriptionally regulate gene expression in a wide variety of eukaryotes. Within organisms, some mature miRNAs, such as paralogous miRNAs, have nearly identical nucleotide sequences, which makes them virtually indistinguishable from one another by conventional hybridization-based approaches. Here we describe two inexpensive, sensitive methods for rapidly discriminating between paralogous miRNAs or other closely related miRNAs and for quantifying their abundance. The first approach is a sequential ribonuclease-protection and primer-extension assay; the second approach is a primer-extension assay that employs short oligonucleotide probes to exacerbate the instability of mismatched probe:miRNA hybrids. Both approaches are rapid and can be easily performed in their entirety using common laboratory equipment. As a proof of concept, we have used these methods to determine the exact identities of the human miR-17 family members that are increased by infection with the intracellular parasite Toxoplasma gondii. These methods can be used to rapidly and inexpensively discriminate between any closely related miRNAs in any organism.

  2. Molecular investigation and phylogeny of Anaplasma spp. in Mediterranean ruminants reveal the presence of neutrophil-tropic strains closely related to A. platys.

    Science.gov (United States)

    Zobba, Rosanna; Anfossi, Antonio G; Pinna Parpaglia, Maria Luisa; Dore, Gian Mario; Chessa, Bernardo; Spezzigu, Antonio; Rocca, Stefano; Visco, Stefano; Pittau, Marco; Alberti, Alberto

    2014-01-01

    Few data are available on the prevalence and molecular typing of species belonging to the genus Anaplasma in Mediterranean ruminants. In this study, PCR analysis and sequencing of both 16S rRNA and groEL genes were combined to investigate the presence, prevalence, and molecular traits of Anaplasma spp. in ruminants sampled on the Island of Sardinia, chosen as a subtropical representative area. The results demonstrate a high prevalence of Anaplasma spp. in ruminants, with animals infected by at least four of six Anaplasma species (Anaplasma marginale, A. bovis, A. ovis, and A. phagocytophilum). Moreover, ruminants host a number of neutrophil-tropic strains genetically closely related to the canine pathogen A. platys. The high Anaplasma spp. prevalence and the identification of as-yet-unclassified neutrophil-tropic strains raise concerns about the specificity of serological tests routinely used in ruminants and provide additional background for reconstructing the evolutionary history of species genetically related to A. phagocytophilum.

  3. Karyotyping of female and male Hediste japonica (Polychaeta, Annelida) in comparison with those of two closely related species, H. diadroma and H. atoka.

    Science.gov (United States)

    Tosuji, Hiroaki; Miyamoto, Junko; Hayata, Yuki; Sato, Masanori

    2004-02-01

    Karyotypes of females and males of the brackish-water polychaete Hediste japonica sensu stricto, collected from the Ariake Sea, Japan, were examined by using regenerating tails. We used the Giemsa staining method and a computer-assisted image-analyzing system for the identification of each chromosome pair. The somatic chromosome number was 2n=28. The presence of an XX-XY (male heterogametic) sex chromosome system was determined from well-spread metaphase plates of somatic cells. The type of sex chromosomes related with phenotype exactly. The metacentric Y chromosome was much larger than the submetacentric X chromosome. All autosomes were metacentric. The karyotype of this species was compared with those of the other two closely related species (H. diadroma and H. atoka). The karyotypes of all the three species were similar to one another.

  4. Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.

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    Albert Lee

    2008-12-01

    Full Text Available A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions and how its transcriptional networks are controlled, and may provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well-studied model eukaryote, we still do not have a full catalog or understanding of all its genes. In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the goal of preferentially increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS to identify, map, and validate unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells. We identified 365 currently unannotated transcripts, the majority presumably representing low abundance or short-lived RNAs, of which 185 are previously unknown and unique to this study. It is likely that many of these are cryptic unstable transcripts (CUTs, which are rapidly degraded and whose function(s within the cell are still unclear, while others may be novel functional transcripts. Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae. Such regions of the genome have typically been less well-studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species.

  5. Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein-RNA complex

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    Alayyoubi, Maher; Leser, George P.; Kors, Christopher A.; Lamb, Robert A. [NWU

    2015-05-20

    Parainfluenza virus 5 (PIV5) is a member of the Paramyxoviridae family of membrane-enveloped viruses with a negative-sense RNA genome that is packaged and protected by long filamentous nucleocapsid-helix structures (RNPs). These RNPs, consisting of ~2,600 protomers of nucleocapsid (N) protein, form the template for viral transcription and replication. We have determined the 3D X-ray crystal structure of the nucleoprotein (N)-RNA complex from PIV5 to 3.11-Å resolution. The structure reveals a 13-mer nucleocapsid ring whose diameter, cavity, and pitch/height dimensions agree with EM data from early studies on the Paramyxovirinae subfamily of native RNPs, indicating that it closely represents one-turn in the building block of the RNP helices. The PIV5-N nucleocapsid ring encapsidates a nuclease resistant 78-nt RNA strand in its positively charged groove formed between the N-terminal (NTD) and C-terminal (CTD) domains of its successive N protomers. Six nucleotides precisely are associated with each N protomer, with alternating three-base-in three-base-out conformation. The binding of six nucleotides per protomer is consistent with the "rule of six" that governs the genome packaging of the Paramyxovirinae subfamily of viruses. PIV5-N protomer subdomains are very similar in structure to the previously solved Nipah-N structure, but with a difference in the angle between NTD/CTD at the RNA hinge region. Based on the Nipah-N structure we modeled a PIV5-N open conformation in which the CTD rotates away from the RNA strand into the inner spacious nucleocapsid-ring cavity. This rotation would expose the RNA for the viral polymerase activity without major disruption of the nucleocapsid structure.

  6. Detection of Inter-lineage Natural Recombination in Avian Paramyxovirus Serotype 1 using Simplified Deep Sequencing Platform

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    Dilan Amila Satharasinghe

    2016-11-01

    Full Text Available Newcastle disease virus (NDV is a prototype member of avian paramyxovirus serotype 1 (APMV-1, which causes severe and contagious disease in the commercial poultry and wild birds. Despite extensive vaccination programs and other control measures, the disease remains endemic around the globe especially in Asia, Africa, and the Middle East. Being a single serotype, genotype II based vaccines remained most acceptable means of immunization. However, the evidence is emerging on failures of vaccines mainly due to evolving nature of the virus and higher genetic gaps between vaccine and field strains of APMV-1. Most of the epidemiological and genetic characterizations of APMVs are based on conventional methods, which are prone to mask the diverse population of viruses in complex samples. In this study, we report the application of a simple, robust, and less resource-demanding methodology for the whole genome sequencing of NDV, using next-generation sequencing on the Illumina MiSeq platform. Using this platform, we sequenced full genomes of five virulent Malaysian NDV strains collected during 2004-2013. All isolates clustered within highly prevalent lineage 5 (specifically in lineage 5a; however, a significantly greater genetic divergence was observed in isolates collected from 2004 to 2011. Interestingly, genetic characterization of one isolate collected in 2013 (IBS025/13 shown natural recombination between lineage 2 and lineage 5. In the event of recombination, the isolate (IBS025/13 carried nucleocapsid protein consist of 55-1801 nucleotides (nts and near-complete phosphoprotein (1804-3254 nts genes of lineage 2 whereas surface glycoproteins (fusion, hemagglutinin-neuraminidase and large polymerase of lineage 5. Additionally, the recombinant virus has a genome size of 15,186 nts which is characteristics for the old genotypes I to IV isolated from 1930 to 1960. Taken together, we report the occurrence of a natural recombination in circulating strains

  7. Genome-wide Identification and Expression Analysis of Calcium-dependent Protein Kinase and Its Closely Related Kinase Genes in Capsicum annuum

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    hanyang ecai

    2015-09-01

    Full Text Available As Ca2+ sensors and effectors, calcium-dependent protein kinases (CDPKs play important roles in regulating the downstream components of calcium signaling, which are ubiquitously involved in plant growth, development, and response to environmental cues. However, no CDPKs have been characterized in Capsicum annuum thus far. Herein, a comprehensive analysis of genes encoding pepper CDPKs and CDPK-related protein kinases (CRKs was performed, and 31 CDPK genes and five closely related kinase genes were identified, which were phylogenetically divided into four distinct subfamilies and unevenly distributed across nine chromosomes. Conserved sequence and exon-intron structures were found to be shared by pepper CDPKs within the same subfamily, and the expansion of the CaCPK family in pepper was found to be due to segmental duplication events. Five CDPKs in the Capsicum annuum variety CM334 were found to be mutated in the Chiltepin variety, and one CDPK present in CM334 was lost in Chiltepin. The majority of CDPK and CRK genes were expressed in different pepper tissues and developmental stages, and 10, 12, and eight CDPK genes were transcriptionally modified by salt, heat, and Ralstonia solanacearum stresses, respectively. Furthermore, these genes were found to respond specifically to one stress as well as respond synergistically to two stresses or three stresses, suggesting that these CDPK genes might be involved in the specific or synergistic response of pepper to salt, heat, and R. solanacearum. Our results lay the foundation for future functional characterization of pepper CDPK and its closely related gene families.

  8. Absence of XMRV and closely related viruses in primary prostate cancer tissues used to derive the XMRV-infected cell line 22Rv1.

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    Jaydip Das Gupta

    Full Text Available The 22Rv1 cell line is widely used for prostate cancer research and other studies throughout the world. These cells were established from a human prostate tumor, CWR22, that was serially passaged in nude mice and selected for androgen independence. The 22Rv1 cells are known to produce high titers of xenotropic murine leukemia virus-related virus (XMRV. Recent studies suggested that XMRV was inadvertently created in the 1990's when two murine leukemia virus (MLV genomes (pre-XMRV1 and pre-XMRV-2 recombined during passaging of the CWR22 tumor in mice. The conclusion that XMRV originated from mice and not the patient was based partly on the failure to detect XMRV in early CWR22 xenografts. While that deduction is certainly justified, we examined the possibility that a closely related virus could have been present in primary tumor tissue. Here we report that we have located the original prostate tumor tissue excised from patient CWR22 and have assayed the corresponding DNA by PCR and the tissue sections by fluorescence in situ hybridization for the presence of XMRV or a similar virus. The primary tumor tissues lacked mouse DNA as determined by PCR for intracisternal A type particle DNA, thus avoiding one of the limitations of studying xenografts. We show that neither XMRV nor a closely related virus was present in primary prostate tissue of patient CWR22. Our findings confirm and reinforce the conclusion that XMRV is a recombinant laboratory-generated mouse virus that is highly adapted for human prostate cancer cells.

  9. Single substitutions to closely related amino acids contribute to the functional diversification of an insect-inducible, positively selected plant cystatin.

    Science.gov (United States)

    Rasoolizadeh, Asieh; Goulet, Marie-Claire; Sainsbury, Frank; Cloutier, Conrad; Michaud, Dominique

    2016-04-01

    A causal link has been reported between positively selected amino acids in plant cystatins and the inhibitory range of these proteins against insect digestive cysteine (Cys) proteases. Here we assessed the impact of single substitutions to closely related amino acids on the contribution of positive selection to cystatin diversification. Cystatin sequence alignments, while confirming hypervariability, indicated a preference for related amino acids at positively selected sites. For example, the non-polar residues leucine (Leu), isoleucine (Ile) and valine (Val) were shown to predominate at positively selected site 2 in the N-terminal region, unlike selected sites 6 and 10, where polar residues are preferred. The model cystatin SlCYS8 and single variants with Leu, Ile or Val at position 2 were compared with regard to their ability to bind digestive proteases of the coleopteran pest Leptinotarsa decemlineata and to induce compensatory responses in this insect. A functional proteomics procedure to capture target Cys proteases in midgut extracts allowed confirmation of distinct binding profiles for the cystatin variants. A shotgun proteomics procedure to monitor whole Cys protease complements revealed protease family specific compensatory responses in the insect, dependent on the variant ingested. Our data confirm the contribution of closely related amino acids to the functional diversity of positively selected plant cystatins in a broader structure/function context imposing physicochemical constraints to primary structure alterations. They also underline the complexity of protease/inhibitor interactions in plant-insect systems, and the challenges still to be met in order to harness the full potential of ectopically expressed protease inhibitors in crop protection.

  10. Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from mtDNA and nuclear markers

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    Schneider Horacio

    2011-09-01

    Full Text Available Abstract Background The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3 we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species. Results All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB, while R. marina sequences from the left Amazon bank (LAB are monophyletic. An Isolation-with-Migration (IM analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene, while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene. This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr, which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies. Conclusions The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these

  11. Two atomic constraints unambiguously position the S4 segment relative to S1 and S2 segments in the closed state of Shaker K channel.

    Science.gov (United States)

    Campos, Fabiana V; Chanda, Baron; Roux, Benoît; Bezanilla, Francisco

    2007-05-01

    It is now well established that the voltage-sensing S4 segment in voltage-dependent ion channels undergoes a conformational change in response to varying membrane potential. However, the magnitude of the movement of S4 relative to the membrane and the rest of the protein remains controversial. Here, by using histidine scanning mutagenesis in the Shaker K channel, we identified mutants I241H (S1 segment) and I287H (S2 segment) that generate inward currents at hyperpolarized potentials, suggesting that these residues are part of a hydrophobic plug that separates the water-accessible crevices. Additional experiments with substituted cysteine residues showed that, at hyperpolarized potentials, both I241C and I287C can spontaneously form disulphide and metal bridges with R362C, the position of the first charge-carrying residue in S4. These results constrain unambiguously the closed-state positions of the S4 segment with respect to the S1 and S2 segments, which are known to undergo little or no movement during gating. To satisfy these constraints, the S4 segment must undergo an axial rotation of approximately 180 degrees and a transmembrane (vertical) movement of approximately 6.5 A at the level of R362 in going from the open to the closed state of the channel, moving the gating charge across a focused electric field.

  12. Bacterial Species-Specific Activity of a Fluoroquinolone against Two Closely Related Pasteurellaceae with Similar MICs: Differential In Vitro Inoculum Effects and In Vivo Efficacies.

    Directory of Open Access Journals (Sweden)

    Guillaume Lhermie

    Full Text Available We investigated the antimicrobial activity of a fluoroquinolone against two genetically close bacterial species belonging to the Pasteurellaceae family. Time-kill experiments were used to measure the in vitro activity of marbofloxacin against two strains of Mannheimia haemolytica and Pasteurella multocida with similar MICs. We observed that marbofloxacin was equally potent against 105 CFU/mL inocula M. haemolytica and P. multocida. However, an inoculum effect was observed with P. multocida, meaning that marbofloxacin activity was decreased against a 108 CFU/mL inoculum, whereas no inoculum effect was observed with M. haemolytica. Marbofloxacin activity was also tested in a lung infection model with immunocompromised mice intratracheally infected with 109 CFU of each bacteria. At the same dose, the clinical and bacteriological outcomes were much better for mice infected with M. haemolytica than for those infected with P. multocida. Moreover, bacteriological eradication was obtained with a lower marbofloxacin dose for mice infected with M. haemolytica. Our results suggest that the differential in vivo marbofloxacin efficacy observed with the two bacterial species of similar MIC could be explained by a differential inoculum effect. Consequently, MICs determined on 105 CFU inocula were not predictive of the differences in antibiotic efficacies against high bacterial inocula of closely related bacterial strains. These results could stimulate further investigations on bacterial species-specific antibiotic doses in a clinical setting.

  13. Bacterial Species-Specific Activity of a Fluoroquinolone against Two Closely Related Pasteurellaceae with Similar MICs: Differential In Vitro Inoculum Effects and In Vivo Efficacies

    Science.gov (United States)

    Lhermie, Guillaume; El Garch, Farid; Toutain, Pierre-Louis; Ferran, Aude A.; Bousquet-Mélou, Alain

    2015-01-01

    We investigated the antimicrobial activity of a fluoroquinolone against two genetically close bacterial species belonging to the Pasteurellaceae family. Time-kill experiments were used to measure the in vitro activity of marbofloxacin against two strains of Mannheimia haemolytica and Pasteurella multocida with similar MICs. We observed that marbofloxacin was equally potent against 105 CFU/mL inocula M. haemolytica and P. multocida. However, an inoculum effect was observed with P. multocida, meaning that marbofloxacin activity was decreased against a 108 CFU/mL inoculum, whereas no inoculum effect was observed with M. haemolytica. Marbofloxacin activity was also tested in a lung infection model with immunocompromised mice intratracheally infected with 109 CFU of each bacteria. At the same dose, the clinical and bacteriological outcomes were much better for mice infected with M. haemolytica than for those infected with P. multocida. Moreover, bacteriological eradication was obtained with a lower marbofloxacin dose for mice infected with M. haemolytica. Our results suggest that the differential in vivo marbofloxacin efficacy observed with the two bacterial species of similar MIC could be explained by a differential inoculum effect. Consequently, MICs determined on 105 CFU inocula were not predictive of the differences in antibiotic efficacies against high bacterial inocula of closely related bacterial strains. These results could stimulate further investigations on bacterial species-specific antibiotic doses in a clinical setting. PMID:26506096

  14. Studies on oil emulsion inactivated vaccine against duck paramyxovirus disease%鸭副黏病毒油乳剂灭活疫苗的制备

    Institute of Scientific and Technical Information of China (English)

    刘霞; 刁有祥; 李秀娟; 李建侠

    2011-01-01

    将分离的鸭副黏病毒,经0.1%的甲醛灭活后与白油、吐温-80、司盘-80,按一定比例混合后在胶体磨中快速乳化成油包水型,制备了鸭副黏病毒油乳佐剂灭活疫苗。并对制备的疫苗进行了物理性状、无菌检验、安全性、稳定性检验、抗体消长规律、交叉免疫保护及免疫效力检验。结果表明,该疫苗安全可靠,注射后鸭的精神状况良好,饮食、粪便无异常变化,注射部位未见明显变化,疫苗吸收良好。免疫后14d即可产生抗体(平均为41og2),60d可达到91og2。免疫后25d攻毒保护率可达90%以上。%The oil emulsion vaccine against duck paramyxovirus was prepared with duck paramyxovirus isolated from duckling.duck paramyxovirus was mixed according to certain ratio with white oil,Tween-80 and Span-80 after being inactivated with 0.1% formaldehyde.And then the mixture was quickly emulsified into water in oil type by the colloid mill.The tests of the physical properties,asepsis inspection,safety test,stability test,antibody titer change rules,cross protection,immunity and effectiveness,etc.of the inactive vaccine were carried out.The results showed that the vaccine had good safety and reliability.The mental condition,eating and feces of ducks had no abnormal changes after the injection of the vaccine.The vaccine was well absorbed and the injection site was without obvious changes.The antibodies against the virus were generated at 14 d and the highest antibodies were generated 60 d after inoculation with 91og2.The protection rate could be up to 90% at 25 d after vaccination.

  15. Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips

    Science.gov (United States)

    Bavykin, Sergei G.; Mirzabekov, Andrei D.

    2007-10-30

    The present invention is directed to a novel method of discriminating a highly infectious bacterium Bacillus anthracis from a group of closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations. The identification and analysis of these sequence variations enables positive discrimination of isolates of the B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed probes, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.

  16. Neuropathological review of 138 cases genetically tested for X-linked hydrocephalus: evidence for closely related clinical entities of unknown molecular bases.

    Science.gov (United States)

    Adle-Biassette, Homa; Saugier-Veber, Pascale; Fallet-Bianco, Catherine; Delezoide, Anne-Lise; Razavi, Férecheté; Drouot, Nathalie; Bazin, Anne; Beaufrère, Anne-Marie; Bessières, Bettina; Blesson, Sophie; Bucourt, Martine; Carles, Dominique; Devisme, Louise; Dijoud, Frédérique; Fabre, Blandine; Fernandez, Carla; Gaillard, Dominique; Gonzales, Marie; Jossic, Frédérique; Joubert, Madeleine; Laurent, Nicole; Leroy, Brigitte; Loeuillet, Laurence; Loget, Philippe; Marcorelles, Pascale; Martinovic, Jelena; Perez, Marie-José; Satge, Daniel; Sinico, Martine; Tosi, Mario; Benichou, Jacques; Gressens, Pierre; Frebourg, Thierry; Laquerrière, Annie

    2013-09-01

    L1 syndrome results from mutations in the L1CAM gene located at Xq28. It encompasses a wide spectrum of diseases, X-linked hydrocephalus being the most severe phenotype detected in utero, and whose pathophysiology is incompletely understood. The aim of this study was to report detailed neuropathological data from patients with mutations, to delineate the neuropathological criteria required for L1CAM gene screening in foetuses by characterizing the sensitivity, specificity and positive predictive value of the cardinal signs, and to discuss the main differential diagnoses in non-mutated foetuses in order to delineate closely related conditions without L1CAM mutations. Neuropathological data from 138 cases referred to our genetic laboratory for screening of the L1CAM gene were retrospectively reviewed. Fifty-seven cases had deleterious L1CAM mutations. Of these, 100 % had hydrocephalus, 88 % adducted thumbs, 98 % pyramidal tract agenesis/hypoplasia, 90 % stenosis of the aqueduct of Sylvius and 68 % agenesis/hypoplasia of the corpus callosum. Two foetuses had L1CAM mutations of unknown significance. Seventy-nine cases had no L1CAM mutations; these were subdivided into four groups: (1) hydrocephalus sometimes associated with corpus callosum agenesis (44 %); (2) atresia/forking of the aqueduct of Sylvius/rhombencephalosynapsis spectrum (27 %); (3) syndromic hydrocephalus (9 %), and (4) phenocopies with no mutations in the L1CAM gene (20 %) and in whom family history strongly suggested an autosomal recessive mode of transmission. These data underline the existence of closely related clinical entities whose molecular bases are currently unknown. The identification of the causative genes would greatly improve our knowledge of the defective pathways involved in these cerebral malformations.

  17. Secondary metabolite profiles and antifungal drug susceptibility of Aspergillus fumigatus and closely related species, Aspergillus lentulus, Aspergillus udagawae, and Aspergillus viridinutans.

    Science.gov (United States)

    Tamiya, Hiroyuki; Ochiai, Eri; Kikuchi, Kazuyo; Yahiro, Maki; Toyotome, Takahito; Watanabe, Akira; Yaguchi, Takashi; Kamei, Katsuhiko

    2015-05-01

    The incidence of Aspergillus infection has been increasing in the past few years. Also, new Aspergillus fumigatus-related species, namely Aspergillus lentulus, Aspergillus udagawae, and Aspergillus viridinutans, were shown to infect humans. These fungi exhibit marked morphological similarities to A. fumigatus, albeit with different clinical courses and antifungal drug susceptibilities. The present study used liquid chromatography/time-of-flight mass spectrometry to identify the secondary metabolites secreted as virulence factors by these Aspergillus species and compared their antifungal susceptibility. The metabolite profiles varied widely among A. fumigatus, A. lentulus, A. udagawae, and A. viridinutans, producing 27, 13, 8, and 11 substances, respectively. Among the mycotoxins, fumifungin, fumiquinazoline A/B and D, fumitremorgin B, gliotoxin, sphingofungins, pseurotins, and verruculogen were only found in A. fumigatus, whereas auranthine was only found in A. lentulus. The amount of gliotoxin, one of the most abundant mycotoxins in A. fumigatus, was negligible in these related species. In addition, they had decreased susceptibility to antifungal agents such as itraconazole and voriconazole, even though metabolites that were shared in the isolates showing higher minimum inhibitory concentrations than epidemiological cutoff values were not detected. These strikingly different secondary metabolite profiles may lead to the development of more discriminative identification protocols for such closely related Aspergillus species as well as improved treatment outcomes.

  18. Study of variations as desired-relative (DELTA), rather than absolute, differences: falsification of the purpose of achieving source-representative and closely comparable lab-results

    CERN Document Server

    Datta, B P

    2014-01-01

    Recently (arXiv:1101.0973), it has been pointed out by us that the possible variation in any source (S) specific elemental isotopic (viz. 2H/1H) abundance ratio SR can more accurately be assessed by its absolute estimate Sr [viz. as (Sr - DR), with D as a standard-source] than by either corresponding measured-relative (S/W-DELTA) estimate ([Sr/Wr] - 1) or DELTA-scale-converted-relative (S/D-DELTA) estimate ([Sr/DR] - 1). Here, we present the fundamentals behind scale-conversion, thereby enabling to understand why at all Sr should be the source- and/ or variation-characterizing key, i.e. why different lab-specific results should be more closely comparable as absolute estimates (SrLab1, SrLab2) than as desired-relative (S/D-DELTALab1, S/D-DELTALab2) estimates. Further, the study clarifies that: (i) the DELTA-scale-conversion (S/W-DELTA into S/D-DELTA, even with the aid of calibrated auxiliary-reference-standard(s) Ai(s)) cannot make the estimates (as S/D-DELTA, and thus Sr) free of the measurement-reference W; ...

  19. Can mixed-species groups reduce individual parasite load? A field test with two closely related poeciliid fishes (Poecilia reticulata and Poecilia picta.

    Directory of Open Access Journals (Sweden)

    Felipe Dargent

    Full Text Available Predation and parasitism are two of the most important sources of mortality in nature. By forming groups, individuals can gain protection against predators but may increase their risk of being infected with contagious parasites. Animals might resolve this conflict by forming mixed-species groups thereby reducing the costs associated with parasites through a relative decrease in available hosts. We tested this hypothesis in a system with two closely related poeciliid fishes (Poecilia reticulata and Poecilia picta and their host-specific monogenean ectoparasites (Gyrodactylus spp. in Trinidad. Fish from three different rivers were sampled from single and mixed-species groups, measured and scanned for Gyrodactylus. The presence and abundance of Gyrodactylus were lower when fish of both species were part of mixed-species groups relative to single-species groups. This is consistent with the hypothesis that mixed-species groups provide a level of protection against contagious parasites. We discuss the importance of potentially confounding factors such as salinity and individual fish size.

  20. Can mixed-species groups reduce individual parasite load? A field test with two closely related poeciliid fishes (Poecilia reticulata and Poecilia picta).

    Science.gov (United States)

    Dargent, Felipe; Torres-Dowdall, Julián; Scott, Marilyn E; Ramnarine, Indar; Fussmann, Gregor F

    2013-01-01

    Predation and parasitism are two of the most important sources of mortality in nature. By forming groups, individuals can gain protection against predators but may increase their risk of being infected with contagious parasites. Animals might resolve this conflict by forming mixed-species groups thereby reducing the costs associated with parasites through a relative decrease in available hosts. We tested this hypothesis in a system with two closely related poeciliid fishes (Poecilia reticulata and Poecilia picta) and their host-specific monogenean ectoparasites (Gyrodactylus spp.) in Trinidad. Fish from three different rivers were sampled from single and mixed-species groups, measured and scanned for Gyrodactylus. The presence and abundance of Gyrodactylus were lower when fish of both species were part of mixed-species groups relative to single-species groups. This is consistent with the hypothesis that mixed-species groups provide a level of protection against contagious parasites. We discuss the importance of potentially confounding factors such as salinity and individual fish size.

  1. Correlation between serum hepatitis B virus core-related antigen and intrahepatic covalently closed circular DNA in chronic hepatitis B patients.

    Science.gov (United States)

    Suzuki, Fumitaka; Miyakoshi, Hideo; Kobayashi, Mariko; Kumada, Hiromitsu

    2009-01-01

    Nucleos(t)ide analogues are utilized for the treatment of chronic HBV infection, and HBe seroconversion and HBV DNA levels are commonly used as markers of viral status and as primary treatment endpoints. Recently, a new assay was prepared for the detection of serum HBV core-related antigen (HBcrAg), consisting of HBcAg, HBeAg, and p22cr, which is a precore protein from amino acid -28 to at least amino acid 150, by coding the precore/core region. In this study, we examined the correlation between serum HBcrAg concentration and viral status by the analysis of serum HBeAg, HBsAg, peripheral HBV DNA, and intrahepatic covalently closed circular DNA (cccDNA) in 57 chronic hepatitis B patients. Intrahepatic cccDNA was detected in all 57 patients, 42 patients were HBcrAg-positive, and serum HBcrAg concentration level was closely correlated with cccDNA. Additionally, positive HBcrAg concentration level results were observed in 6 out of 13 HBsAg seroclearance patients and 20 out of 31 HBV DNA-negative patients. Moreover, the correlation between HBcrAg and cccDNA in these 31 HBV DNA-negative patients was statistically significant (r = 0.482, P = 0.006). These data suggest that serum HBcrAg concentration is well correlated with intrahepatic cccDNA level, and that the measurement of serum HBcrAg may be clinically useful for monitoring intrahepatic HBV viral status, especially in patients under treatment with nucleos(t)ide analogues.

  2. Asymmetric female preferences for courtship pheromones in two closely-related newt species, the smooth newt (Lissotriton vulgaris) and the Carpathian newt (L. montandoni) (Salamandridae).

    Science.gov (United States)

    Osikowski, Artur

    2012-06-01

    The smooth (Lissotriton vulgaris) and Carpathian (L. montandoni) newts are sister species. These are separated by a moderate genetic distance, but exhibit striking morphological differences, especially in male epigamic traits. In the areas where they co-occur, they readily mate with each other and produce viable hybrids. However, a high level of pre-zygotic isolation with an unknown behavioral basis has been reported. The complex courtship of newts consists of at least three types of modality: chemical, visual, and tactile. The relative significance of these in mate choice is unclear, but it is commonly accepted that pheromones are an important communication channel. The goal of this study was to determine whether the females of L. vulgaris and L. montandoni exhibit preferences for conspecific extracts from the pheromone-producing abdominal (dorsal) glands. Females of both species spent more time in proximity to the source of the abdominal gland extracts of their own species when a liver extract was presented as an alternative. In a second trial, females were simultaneously confronted with conspecific and heterospecific abdominal gland extracts. Asymmetric preferences were found. Lissotriton vulgaris females were not selective, whereas L. montandoni females preferred the conspecific abdominal gland extract. This finding is consistent with the results of earlier experiments on mate choice in these species. The results strongly indicate that pheromones play a crucial role in courtship and species recognition in this pair of closely related, hybridizing species.

  3. The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements.

    Science.gov (United States)

    Sheibani-Tezerji, Raheleh; Naveed, Muhammad; Jehl, Marc-André; Sessitsch, Angela; Rattei, Thomas; Mitter, Birgit

    2015-01-01

    The seed as a habitat for microorganisms is as yet under-explored and has quite distinct characteristics as compared to other vegetative plant tissues. In this study, we investigated three closely related P. ananatis strains (named S6, S7, and S8), which were isolated from maize seeds of healthy plants. Plant inoculation experiments revealed that each of these strains exhibited a different phenotype ranging from weak pathogenic (S7), commensal (S8), to a beneficial, growth-promoting effect (S6) in maize. We performed a comparative genomics analysis in order to find genetic determinants responsible for the differences observed. Recent studies provided exciting insight into the genetic drivers of niche adaption and functional diversification of the genus Pantoea. However, we report here for the first time on the analysis of P. ananatis strains colonizing the same ecological niche but showing distinct interaction strategies with the host plant. Our comparative analysis revealed that genomes of these three strains are highly similar. However, genomic differences in genes encoding protein secretion systems and putative effectors, and transposase/integrases/phage related genes could be observed.

  4. The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements

    Directory of Open Access Journals (Sweden)

    Raheleh eSheibani-Tezerji

    2015-05-01

    Full Text Available The seed as a habitat for microorganisms is as yet under-explored and has quite distinct characteristics as compared to other vegetative plant tissues. In this study, we investigated three closely related P. ananatis strains (named S6, S7 and S8, which were isolated from maize seeds of healthy plants. Plant inoculation experiments revealed that each of these strains exhibited a different phenotype ranging from weak pathogenic (S7, commensal (S8, to a beneficial, growth-promoting effect (S6 in maize. We performed a comparative genomics analysis in order to find genetic determinants responsible for the differences observed. Recent studies provided exciting insight into the genetic drivers of niche adaption and functional diversification of the genus Pantoea. However, we report here for the first time on the analysis of P. ananatis strains colonizing the same ecological niche but showing distinct interaction strategies with the host plant. Our comparative analysis revealed that genomes of these three strains are highly similar. However, genomic differences in genes encoding protein secretion systems and putative effectors, and transposase/integrases/phage related genes could be observed.

  5. Paramyxovirus Infection Mimics In Vivo Cellular Dynamics in Three-Demensional Human Bronchio-Epithelial Tissue-Like Assemblies

    Science.gov (United States)

    Deatly, Anne M.; Lin, Yen-Huei; McCarthy, Maureen; Chen, Wei; Miller, Lynn Z.; Quiroz, Jorge; Nowak, Becky M.; Lerch, Robert A.; Udem, Stephen A.; Goodwin, Thomas J.

    2012-01-01

    Respiratory syncytial virus and parainfluenza virus cause severe respiratory disease, especially in infants, children and the elderly. An in vitro model that accurately mimics infection of the human respiratory epithelium (HRE) would facilitate vaccine development greatly. Monolayer cultures traditionally used to study these viruses do not accurately and precisely differentiate the replication efficiencies of wild type and attenuated viruses. Therefore, we engineered novel three-dimensional (3D) tissue-like assemblies (TLAs) of human broncho-epithelial (HBE) cells to produce a more physiologically relevant in vitro model of the HRE. TLAs resemble HRE structurally and by expression of differentiated epithelial cell markers. Most significantly, wild type viruses exhibited a clear growth advantage over attenuated strains in TLAs unlike monolayer cultures. In addition, the TLAs responded to virus infection by secreting pro-inflammatory mediators similar to the respiratory epithelia of infected children. These characteristics make the TLA model a valuable platform technology to develop and evaluate live, attenuated respiratory virus vaccine candidates for human use. Respiratory virus diseases, the most frequent and least preventable of all infectious diseases, range in severity from the common cold to severe bronchiolitis and pneumonia . Two paramyxoviruses, respiratory syncytial virus (RSV) and parainfluenza virus type 3 (PIV3), are responsible for a majority of the most severe respiratory diseases of infants and young children. RSV causes 70% of all bronchiolitis cases and is a major cause of morbidity and mortality worldwide, especially in infants. PIV3 causes 10-15% of bronchiolitis and pneumonia during infancy, second only to RSV, and 40% of croup in infants To date, licensed vaccines are not available to prevent these respiratory diseases. At present, traditional monkey kidney (Vero and LLC-MK2) and human (HEp-2) tissue culture cells and small animal models (mouse

  6. The IAB Iron-Meteorite Complex: A Group, Five Subgroups, Numerous Grouplets, Closely Related, Mainly Formed by Crystal Segregation in Rapidly Cooling Melts

    Science.gov (United States)

    Wasson, J. T.; Kallemeyn, G. W.

    2002-01-01

    We present new data or iron meteorites that are members of group IAB or are closely related to this large group, and we have also reevaluated some of our earlier data for these irons. In the past it was not possible to distinguish IAB and IIICD irons on the basis of their positions on element-Ni diagrams. We now find that plotting, the new and revised data yields six sets of compact fields on element-Au diagrams, each set corresponding to a compositional group. The largest set includes the majority (approximately equal to 70) of irons previously designated IA: We christened this set the IAB main group. The remaining five sets we designate subgroups within the IAB complex. Three of these subgroups have Au contents similar to the main group, and form parallel trends in most element-Ni diagrams. The groups originally designated IIIC and IIID are two of these subgroups: they are now well resolved from each other and from the main group. The other low-Au subgroup has Ni contents just above the main group. Two other IAB subgroups have appreciably higher Au contents than the main group and show weaker compositional links to it. We have named these five subgroups on the basis of their Au and Ni contents. The three subgroups having Au contents similar to the main group are the low-Au (L) subgroups the two others the high-Au (H) subgroups. The Ni contents are designated high (H), medium (M), or low (L). Thus the old group IIID is now the sLH subgroup. the old group IIIC is the sLM subgroup. In addition, eight irons assigned to two grouplets plot between sLL and sLM on most element-Au diagrams. A large number (27) of related irons plot outside these compact fields but nonetheless appear to be sufficiently related to also be included in the IAB complex.

  7. Extensive inter- and intraspecific venom variation in closely related parasites targeting the same host: the case of Leptopilina parasitoids of Drosophila.

    Science.gov (United States)

    Colinet, Dominique; Deleury, Emeline; Anselme, Caroline; Cazes, Dominique; Poulain, Julie; Azema-Dossat, Carole; Belghazi, Maya; Gatti, Jean-Luc; Poirié, Marylène

    2013-07-01

    The arms race between immune suppressive parasites that produce virulence factors and hosts that evolve resistance to these factors is suggested to be a key driver for the diversification of both partners. However, little is known regarding the diversity of virulence factors in closely related parasites or the mechanisms underlying the variation of virulence. One of the best-described model to address this issue is the interaction between Leptopilina parasitic wasps and their Drosophila hosts, in which variation of virulence is well documented. Thanks to a combined transcriptomic and proteomic approach, we have identified the main secreted proteins in the venom of Leptopilina heterotoma (Gotheron strain, 66 proteins) and of two well-characterized strains of Leptopilina boulardi, ISm and ISy (65 and 49 proteins, respectively). Results revealed significant quantitative differences in venom components between the L. boulardi strains, in agreement with their different virulence properties. Strikingly, the two related Leptopilina species did not share any abundant venom protein. The main identified proteins in L. boulardi were RhoGAPs and serpins while an aspartylglucosaminidase (AGA) was found abundant in L. heterotoma. The extensive quantitative variation observed between these species may be related with their use of different virulence strategies and/or to differences in their host range (specialist versus generalist). Altogether, our data suggests that parasitoid venom can quickly evolve, mainly through rapid changes in regulation of gene expression. It also evidences venom evolutionary processes largely described in other venomous animals i.e. the convergent recruitment of venom proteins between phylogenetically unrelated organisms, and the role of duplications in the emergence of multigenic families of virulence factors.

  8. Brain spontaneous fluctuations in sensorimotor regions were directly related to eyes open and eyes closed: evidences from a machine learning approach

    Directory of Open Access Journals (Sweden)

    Bishan eLiang

    2014-08-01

    Full Text Available Previous studies have demonstrated that the difference between resting-state brain activations depends on whether the subject was eyes open (EO or eyes closed (EC. However, whether the spontaneous fluctuations are directly related to these two different resting states are still largely unclear. In the present study, we acquired resting-state functional magnetic resonance imaging data from 24 healthy subjects (11 males, 20.17 ± 2.74 years under the EO and EC states. The amplitude of the spontaneous brain activity in low-frequency band was subsequently investigated by using the metric of fractional amplitude of low frequency fluctuation (fALFF for each subject under each state. A support vector machine (SVM analysis was then applied to evaluate whether the category of resting states could be determined from the brain spontaneous fluctuations. We demonstrated that these two resting states could be decoded from the identified pattern of brain spontaneous fluctuations, predominantly based on fALFF in the sensorimotor module. Specifically, we observed prominent relationships between increased fALFF for EC and decreased fALFF for EO in sensorimotor regions. Overall, the present results indicate that a SVM performs well in the discrimination between the brain spontaneous fluctuations of distinct resting states and provide new insight into the neural substrate of the resting states during EC and EO.

  9. Towards harmonised procedures in wildlife epidemiological investigations: a serosurvey of infection with Mycobacterium bovis and closely related agents in wild boar (Sus scrofa) in Switzerland.

    Science.gov (United States)

    Beerli, Olivia; Blatter, Sohvi; Boadella, Mariana; Schöning, Janne; Schmitt, Sarah; Ryser-Degiorgis, Marie-Pierre

    2015-01-01

    Bovine tuberculosis (bTB) is a (re-)emerging disease in European countries, including Switzerland. This study assesses the seroprevalence of infection with Mycobacterium bovis and closely related agents in wild boar (Sus scrofa) in Switzerland, because wild boar are potential maintenance hosts of these pathogens. The study employs harmonised laboratory methods to facilitate comparison with the situation in other countries. Eighteen out of 743 blood samples tested seropositive (2.4%, CI: 1.5-3.9%) by ELISA, and the results for 61 animals previously assessed using culture and PCR indicated that this serological test was not 100% specific for M. bovis, cross-reacting with M. microti. Nevertheless, serology appears to be an appropriate test methodology in the harmonisation of wild boar testing throughout Europe. In accordance with previous findings, the low seroprevalence found in wild boar suggests wildlife is an unlikely source of the M. bovis infections recently detected in cattle in Switzerland. This finding contrasts with the epidemiological situation pertaining in southern Spain.

  10. Heterogeneity in ess transcriptional organization and variable contribution of the Ess/Type VII protein secretion system to virulence across closely related Staphylocccus aureus strains.

    Science.gov (United States)

    Kneuper, Holger; Cao, Zhen Ping; Twomey, Kate B; Zoltner, Martin; Jäger, Franziska; Cargill, James S; Chalmers, James; van der Kooi-Pol, Magdalena M; van Dijl, Jan Maarten; Ryan, Robert P; Hunter, William N; Palmer, Tracy

    2014-09-01

    The Type VII protein secretion system, found in Gram-positive bacteria, secretes small proteins, containing a conserved W-x-G amino acid sequence motif, to the growth medium. Staphylococcus aureus has a conserved Type VII secretion system, termed Ess, which is dispensable for laboratory growth but required for virulence. In this study we show that there are unexpected differences in the organization of the ess gene cluster between closely related strains of S. aureus. We further show that in laboratory growth medium different strains of S. aureus secrete the EsxA and EsxC substrate proteins at different growth points, and that the Ess system in strain Newman is inactive under these conditions. Systematic deletion analysis in S. aureus RN6390 is consistent with the EsaA, EsaB, EssA, EssB, EssC and EsxA proteins comprising core components of the secretion machinery in this strain. Finally we demonstrate that the Ess secretion machinery of two S. aureus strains, RN6390 and COL, is important for nasal colonization and virulence in the murine lung pneumonia model. Surprisingly, however, the secretion system plays no role in the virulence of strain SA113 under the same conditions.

  11. Molecular analyses of a potentially novel Anaplasma species closely related to Anaplasma phagocytophilum detected in sika deer (Cervus nippon yesoensis) in Japan.

    Science.gov (United States)

    Ybañez, Adrian P; Matsumoto, Kotaro; Kishimoto, Toshio; Inokuma, Hisashi

    2012-05-25

    An Anaplasma species closely related to Anaplasma phagocytophilum detected in sika deer in Hokkaido, Japan was molecularly analyzed using 16S rRNA, citrate synthase (gltA), and heat-shock operon (groEL) gene sequences. Genome walking was performed to determine its complete gltA and groEL sequences (1233 bp and 1650 bp, respectively). Percent identities to the closest A. phagocytophilum sequences from the US and European strains were 98.6-98.8%, 76.5%, and 80.3-80.8% for 16S rRNA, gltA, and groEL genes, respectively. For deduced amino acid sequences, percent identities to the closest A. phagocytophilum sequences were 66.7% and 97.6% for gltA and groEL genes, respectively. Phylogenetic analyses revealed divergence from any known A. phagocytophilum strain. The lower identities and the divergent phylogenetic position of the Anaplasma sp. detected from sika deer in Japan with established A. phagocytophilum strains provide evidence of its potential novelty. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. A novel PCR-RFLP assay for molecular characterization of Echinococcus granulosus sensu lato and closely related species in developing countries.

    Science.gov (United States)

    Chaâbane-Banaoues, Raja; Oudni-M'rad, Myriam; M'rad, Selim; Amani, Hizem; Mezhoud, Habib; Babba, Hamouda

    2016-10-01

    Cystic echinococcosis, due to Echinococcus granulosus sensu lato (s. l.), currently affects three million people, especially in low-income countries and results in high livestock production loss. DNA-based methods demonstrated genetic variability of E. granulosus s. l., and five species were recognized to belong to the complex, including E. granulosus sensu stricto (s.s) (genotypes G1-G3), Echinococcus equinus (genotype G4), Echinococcus ortleppi (genotype G5), Echinococcus canadensis (genotypes G6-G10), and the lion strain Echinococcus felidis. The characterization of Echinococcus species responsible for human and animal echinococcosis is crucial to adapt the preventive measures against this parasitic disease. The sequencing approach is the gold standard for genotyping assays. Unfortunately, developing countries do not often have access to these techniques. Based on in silico RFLP tools, we described an accurate PCR-RFLP method for Echinococcus spp. characterization. The double digestion with the HaeIII and HinfI restriction enzymes of the PCR product from nad1 gene (1071 bp) led to a clear discrimination between E. granulosus s. l. and most closely related species (Echinococcus shiquicus and Echinococcus multilocularis).Molecular procedures and phylogenetic analysis confirmed the efficiency and the reproducibility of this simple and fast PCR-RFLP method. This technique is proved useful for fresh/unfixed and FF-PET tissues and enables large-scale molecular epidemiological screening in developing countries.

  13. Description of larvae of two closely related species Cassida palaestina Reiche, 1858 and Cassida rubiginosa Müller, 1776 (Coleoptera: Chrysomelidae: Cassidinae).

    Science.gov (United States)

    Swiętojańska, Jolanta; Moradian, Hossein; Borowiec, Lech; Ostovan, Hadi

    2013-11-29

    Larvae of two closely related species Cassida palaestina Reiche, 1858 and Cassida rubiginosa Müller, 1776 are described in detail including SEM microstructures. First instars are extremely similar with no clear diagnostic characters, larvae of Cassida palaestina are slightly more contrastingly coloured than larvae of C. rubiginosa, the latter having darker scoli, basal part of supra-anal processes and legs. Last instars differ in very subtle but constant characters: lateral scoli of C. palaestina are slightly shorter than those of C. rubiginosa, in C. palaestina tops of the lateral branches are armed apically with an elongate cauliflower-shaped sensillum while in C. rubiginosa tops of the lateral branches are more often armed with a pointed seta than with an elongate cauliflower-shaped sensillum, and cauliflower-shaped sensilla on tergites are less elongate in C. palaestina than in C. rubiginosa. These differences accompanied by distinguishing characters of adults and their distribution range indicate that both taxa are probably vicariant species with partial parapatric occurrence. Centaurea behen is a new host plant for C. palaestina.

  14. Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the megavirus lineage.

    Science.gov (United States)

    Yoosuf, Niyaz; Yutin, Natalya; Colson, Philippe; Shabalina, Svetlana A; Pagnier, Isabelle; Robert, Catherine; Azza, Said; Klose, Thomas; Wong, Jimson; Rossmann, Michael G; La Scola, Bernard; Raoult, Didier; Koonin, Eugene V

    2012-01-01

    The 1,021,348 base pair genome sequence of the Acanthamoeba polyphaga moumouvirus, a new member of the Mimiviridae family infecting Acanthamoeba polyphaga, is reported. The moumouvirus represents a third lineage beside mimivirus and megavirus. Thereby, it is a new member of the recently proposed Megavirales order. This giant virus was isolated from a cooling tower water in southeastern France but is most closely related to Megavirus chiliensis, which was isolated from ocean water off the coast of Chile. The moumouvirus is predicted to encode 930 proteins, of which 879 have detectable homologs. Among these predicted proteins, for 702 the closest homolog was detected in Megavirus chiliensis, with the median amino acid sequence identity of 62%. The evolutionary affinity of moumouvirus and megavirus was further supported by phylogenetic tree analysis of conserved genes. The moumouvirus and megavirus genomes share near perfect orthologous gene collinearity in the central part of the genome, with the variations concentrated in the terminal regions. In addition, genomic comparisons of the Mimiviridae reveal substantial gene loss in the moumouvirus lineage. The majority of the remaining moumouvirus proteins are most similar to homologs from other Mimiviridae members, and for 27 genes the closest homolog was found in bacteria. Phylogenetic analysis of these genes supported gene acquisition from diverse bacteria after the separation of the moumouvirus and megavirus lineages. Comparative genome analysis of the three lineages of the Mimiviridae revealed significant mobility of Group I self-splicing introns, with the highest intron content observed in the moumouvirus genome.

  15. Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa.

    Science.gov (United States)

    Ahmed, Ibrar; Matthews, Peter J; Biggs, Patrick J; Naeem, Muhammad; McLenachan, Patricia A; Lockhart, Peter J

    2013-09-01

    Recently, we reported the chloroplast genome-wide association of oligonucleotide repeats, indels and nucleotide substitutions in aroid chloroplast genomes. We hypothesized that the distribution of oligonucleotide repeat sequences in a single representative genome can be used to identify mutational hotspots and loci suitable for population genetic, phylogenetic and phylogeographic studies. Using information on the location of oligonucleotide repeats in the chloroplast genome of taro (Colocasia esculenta), we designed 30 primer pairs to amplify and sequence polymorphic loci. The primers have been tested in a range of intra-specific to intergeneric comparisons, including ten taro samples (Colocasia esculenta) from diverse geographical locations, four other Colocasia species (C. affinis, C. fallax, C. formosana, C. gigantea) and three other aroid genera (represented by Remusatia vivipara, Alocasia brisbanensis and Amorphophallus konjac). Multiple sequence alignments for the intra-specific comparison revealed nucleotide substitutions (point mutations) at all 30 loci and microsatellite polymorphisms at 14 loci. The primer pairs reported here reveal levels of genetic variation suitable for high-resolution phylogeographic and evolutionary studies of taro and other closely related aroids. Our results confirm that information on repeat distribution can be used to identify loci suitable for such studies, and we expect that this approach can be used in other plant groups.

  16. Gray mold populations in german strawberry fields are resistant to multiple fungicides and dominated by a novel clade closely related to Botrytis cinerea.

    Science.gov (United States)

    Leroch, Michaela; Plesken, Cecilia; Weber, Roland W S; Kauff, Frank; Scalliet, Gabriel; Hahn, Matthias

    2013-01-01

    The gray mold fungus Botrytis cinerea is a major threat to fruit and vegetable production. Strawberry fields usually receive several fungicide treatments against Botrytis per season. Gray mold isolates from several German strawberry-growing regions were analyzed to determine their sensitivity against botryticides. Fungicide resistance was commonly observed, with many isolates possessing resistance to multiple (up to six) fungicides. A stronger variant of the previously described multidrug resistance (MDR) phenotype MDR1, called MDR1h, was found to be widely distributed, conferring increased partial resistance to two important botryticides, cyprodinil and fludioxonil. A 3-bp deletion mutation in a transcription factor-encoding gene, mrr1, was found to be correlated with MDR1h. All MDR1h isolates and the majority of isolates with resistance to multiple fungicides were found to be genetically distinct. Multiple-gene sequencing confirmed that they belong to a novel clade, called Botrytis group S, which is closely related to B. cinerea and the host-specific species B. fabae. Isolates of Botrytis group S genotypes were found to be widespread in all German strawberry-growing regions but almost absent from vineyards. Our data indicate a clear subdivision of gray mold populations, which are differentially distributed according to their host preference and adaptation to chemical treatments.

  17. Identification of Enterobacter sakazakii from closely related species: The use of Artificial Neural Networks in the analysis of biochemical and 16S rDNA data

    Directory of Open Access Journals (Sweden)

    Waddington Michael

    2006-03-01

    Full Text Available Abstract Background Enterobacter sakazakii is an emergent pathogen associated with ingestion of infant formula and accurate identification is important in both industrial and clinical settings. Bacterial species can be difficult to accurately characterise from complex biochemical datasets and computer algorithms can potentially simplify the process. Results Artificial Neural Networks were applied to biochemical and 16S rDNA data derived from 282 strains of Enterobacteriaceae, including 189 E. sakazakii isolates, in order to identify key characteristics which could improve the identification of E. sakazakii. The models developed resulted in a predictive performance for blind (validation data of 99.3 % correct discrimination between E. sakazakii and closely related species for both phenotypic and genotypic data. Three main regions of the partial rDNA sequence were found to be key in discriminating the species. Comparison between E. sakazakii and other strains also constitutively positive for expression of the enzyme α-glucosidase resulted in a predictive performance of 98.7 % for 16S rDNA sequence data and 100% for phenotypic data. Conclusion The computationally based methods developed here show a remarkable ability in reducing data dimensionality and complexity, in order to eliminate noise from the system in order to facilitate the speed and reliability of a potential strain identification system. Furthermore, the approaches described are also able to provide valuable information regarding the population structure and distribution of individual species thus providing the foundations for novel assays and diagnostic tests for rapid identification of pathogens.

  18. A phylogenetic lineage of closely related trypanosomes (Trypanosomatidae, Kinetoplastida) of anurans and sand flies (Psychodidae, Diptera) sharing the same ecotopes in brazilian amazonia.

    Science.gov (United States)

    Ferreira, Robson C; De Souza, Adelson A; Freitas, Rui A; Campaner, Marta; Takata, Carmem S A; Barrett, Toby V; Shaw, Jeffrey J; Teixeira, Marta M G

    2008-01-01

    Analysis of the phylogenetic relationships among trypanosomes from vertebrates and invertebrates disclosed a new lineage of trypanosomes circulating among anurans and sand flies that share the same ecotopes in Brazilian Amazonia. This assemblage of closely related trypanosomes was determined by comparing whole SSU rDNA sequences of anuran trypanosomes from the Brazilian biomes of Amazonia, the Pantanal, and the Atlantic Forest and from Europe, North America, and Africa, and from trypanosomes of sand flies from Amazonia. Phylogenetic trees based on maximum likelihood and parsimony corroborated the positioning of all new anuran trypanosomes in the aquatic clade but did not support the monophyly of anuran trypanosomes. However, all analyses always supported four major clades (An01-04) of anuran trypanosomes. Clade An04 is composed of trypanosomes from exotic anurans. Isolates in clades An01 and An02 were from Brazilian frogs and toads captured in the three biomes studied, Amazonia, the Pantanal and the Atlantic Forest. Clade An01 contains mostly isolates from Hylidae whereas clade An02 comprises mostly isolates from Bufonidae; and clade An03 contains trypanosomes from sand flies and anurans of Bufonidae, Leptodactylidae, and Leiuperidae exclusively from Amazonia. To our knowledge, this is the first study describing morphological and growth features, and molecular phylogenetic affiliation of trypanosomes from anurans and phlebotomines, incriminating these flies as invertebrate hosts and probably also as important vectors of Amazonian terrestrial anuran trypanosomes.

  19. Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.).

    Science.gov (United States)

    Wachowiak, Witold; Palmé, Anna E; Savolainen, Outi

    2011-04-01

    Nucleotide polymorphisms at genomic regions including 17 nuclear loci, two chloroplast and one mitochondrial DNA fragments were used to study the speciation history of three pine species: dwarf mountain pine (Pinus mugo), peat-bog pine (P. uliginosa) and Scots pine (P. sylvestris). We set out to investigate three specific speciation scenarios: (I) P. uliginosa is a homoploid hybrid between the other two, (II) the species have evolved without gene flow after divergence and (III) there has been substantial gene flow between the species since their divergence. Overall, the genetic data suggest that P. mugo and P. uliginosa share the same gene pool (average net divergence of 0.0001) and that the phenotypic differences (e.g. growth form) are most likely due to very limited areas of the genome. P. mugo and P. uliginosa are more diverged from P. sylvestris than from each other (average net divergence of 0.0027 and 0.0026, respectively). The nucleotide patterns can best be explained by the divergence with migration speciation scenario, although the hybrid speciation scenario with small genomic contribution from P. sylvestris cannot be completely ruled out. We suggest that the large amount of shared polymorphisms between the pine taxa and the lack of monophyly at all loci studied between P. sylvestris and P. mugo-P. uliginosa can largely be explained by relatively recent speciation history and large effective population sizes but also by interspecific gene flow. These closely related pine taxa form an excellent system for searching for loci involved in adaptive variation as they are differentiated in phenotype and ecology but have very similar genetic background.

  20. Genetic relationships and variation in reproductive strategies in four closely related bromeliads adapted to neotropical ‘inselbergs’: Alcantarea glaziouana, A. regina, A. geniculata and A. imperialis (Bromeliaceae)

    Science.gov (United States)

    Barbará, Thelma; Martinelli, Gustavo; Palma-Silva, Clarisse; Fay, Michael F.; Mayo, Simon; Lexer, Christian

    2009-01-01

    Background and Aims Bromeliads (Bromeliaceae) adapted to rock outcrops or ‘inselbergs’ in neotropical rain forests have been identified as suitable plant models for studying population divergence and speciation during continental plant radiations. Little is known about genetic relationships and variation in reproductive strategies within and among inselberg-adapted species, yet knowledge of these parameters is important for understanding divergence processes and for conservation planning. Methods Nuclear microsatellites were used to assess the role of clonal reproduction, estimate genetic diversity and explore genetic relationships and variation in reproductive strategies for a total of 15 populations of four closely related Alcantarea inselberg species in south-eastern Brazil: A. glaziouana, A. regina, A. geniculata and A. imperialis. Key Results Clonal propagation is frequent in coastal populations of A. glaziouana and A. regina, but absent in the high-altitude species A. geniculata and A. imperialis. Considerable variation in clonal diversity, gene diversity (He), allelic richness, and Wright's inbreeding coefficient (FIS) exists within and between species of Alcantarea. A Bayesian analysis of coastal inselberg species indicated pronounced genetic structure. A neighbor-joining analysis grouped populations of each species together with moderate bootstrap support, except for the high altitude species A. imperialis. Conclusions The coastal inselberg species A. glaziouana and A. regina tend to propagate asexually via vegetative clonal growth, and both reproductive strategies and breeding systems vary greatly between populations and species of Alcantarea. The microsatellite data indicate a history of hybridization and reticulation involving the high-altitude species A. geniculata and A. imperialis in areas of co-occurrence. The results highlight the need to understand similarities and differences in reproductive strategies both within and between related species

  1. Species-level determination of closely related araucarian resins using FTIR spectroscopy and its implications for the provenance of New Zealand amber

    Directory of Open Access Journals (Sweden)

    Leyla J. Seyfullah

    2015-07-01

    Full Text Available Some higher plants, both angiosperms and gymnosperms, can produce resins and some of these resins can polymerize and fossilize to form ambers. Various physical and chemical techniques have been used to identify and profile different plant resins and have then been applied to fossilized resins (ambers, to try to detect their parent plant affinities and understand the process of polymerization, with varying levels of success. Here we focus on resins produced from today’s most resinous conifer family, the Araucariaceae, which are thought to be the parent plants of some of the Southern Hemisphere’s fossil resin deposits. Fourier transform infrared (FTIR spectra of the resins of closely related Araucariaceae species were examined to test whether they could be distinguished at genus and species level and whether the results could then be used to infer the parent plant of a New Zealand amber. The resin FTIR spectra are distinguishable from each other, and the three Araucaria species sampled produced similar FTIR spectra, to which Wollemia resin is most similar. Interspecific variability of the FTIR spectra is greatest in the three Agathis species tested. The New Zealand amber sample is similar in key shared features with the resin samples, but it does differ from the extant resin samples in key distinguishing features, nonetheless it is most similar to the resin of Agathis australis in this dataset. However on comparison with previously published FTIR spectra of similar aged amber and older (Eocene resinites both found in coals from New Zealand and fresh Agathis australis resin, our amber has some features that imply a relatively immature resin, which was not expected from an amber of the Miocene age.

  2. Identification of distinct quantitative trait loci associated with defence against the closely related aphids Acyrthosiphon pisum and A. kondoi in Medicago truncatula

    KAUST Repository

    Guo, Su-Min

    2012-03-21

    Aphids are a major family of plant insect pests. Medicago truncatula and Acyrthosiphon pisum (pea aphid, PA) are model species with a suite of resources available to help dissect the mechanism underlying plant-aphid interactions. A previous study focused on monogenic and relatively strong resistance in M. truncatula to PA and other aphid species. In this study a moderate resistance to PA was characterized in detail in the M. truncatula line A17 and compared with the highly susceptible line A20 and the more resistant line Jester. The results show that PA resistance in A17 involves both antibiosis and tolerance, and that resistance is phloem based. Quantitative trait locus (QTL) analysis using a recombinant inbred line (RIL) population (n=114) from a cross between A17 and A20 revealed that one locus, which co-segregated with AIN (Acyrthosiphon-induced necrosis) on chromosome 3, is responsible for the reduction of aphid biomass (indicator of antibiosis) for both PA and bluegreen aphid (BGA, A. kondoi), albeit to a lesser degree for PA than BGA. Interestingly, two independent loci on chromosomes 5 and 3 were identified for the plant biomass reduction (indicator of plant tolerance) by PA and BGA, respectively, demonstrating that the plant\\'s tolerance response to these two closely related aphid species is distinct. Together with previously identified major resistant (R) genes, the QTLs identified in this study are powerful tools to understand fully the spectrum of plant defence against sap-sucking insects and provide opportunities for breeders to generate effective and sustainable strategies for aphid control. 2012 The Author.

  3. Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286 and comparison to the closely related pathogen Tannerella forsythia.

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    Clifford J Beall

    Full Text Available The uncultivated bacterium Tannerella BU063 (oral taxon 286 is the closest relative to the periodontal pathogen Tannerella forsythia, but is not disease-associated itself. Using a single cell genomics approach, we isolated 12 individual BU063 cells by flow cytometry, and we amplified and sequenced their genomes. Comparative analyses of the assembled genomic scaffolds and their gene contents allowed us to study the diversity of this taxon within the oral community of a single human donor that provided the sample. Eight different BU063 genotypes were represented, all about 5% divergent at the nucleotide level. There were 2 pairs of cells and one group of three that were more highly identical, and may represent clonal populations. We did pooled assemblies on the nearly identical genomes to increase the assembled genomic coverage. The presence of a set of 66 "core" housekeeping genes showed that two of the single cell assemblies and the assembly derived from the three putatively identical cells were essentially complete. As expected, the genome of BU063 is more similar to Tannerella forsythia than any other known genome, although there are significant differences, including a 44% difference in gene content, changes in metabolic pathways, loss of synteny, and an 8-9% difference in GC content. Several identified virulence genes of T. forsythia are not found in BU063 including karilysin, prtH, and bspA. The absence of these genes may explain the lack of periodontal pathogenesis by this species and provides a new foundation to further understand the genome evolution and mechanisms of bacterial-host interaction in closely related oral microbes with different pathogenicity potential.

  4. Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia.

    Science.gov (United States)

    Beall, Clifford J; Campbell, Alisha G; Dayeh, Daniel M; Griffen, Ann L; Podar, Mircea; Leys, Eugene J

    2014-01-01

    The uncultivated bacterium Tannerella BU063 (oral taxon 286) is the closest relative to the periodontal pathogen Tannerella forsythia, but is not disease-associated itself. Using a single cell genomics approach, we isolated 12 individual BU063 cells by flow cytometry, and we amplified and sequenced their genomes. Comparative analyses of the assembled genomic scaffolds and their gene contents allowed us to study the diversity of this taxon within the oral community of a single human donor that provided the sample. Eight different BU063 genotypes were represented, all about 5% divergent at the nucleotide level. There were 2 pairs of cells and one group of three that were more highly identical, and may represent clonal populations. We did pooled assemblies on the nearly identical genomes to increase the assembled genomic coverage. The presence of a set of 66 "core" housekeeping genes showed that two of the single cell assemblies and the assembly derived from the three putatively identical cells were essentially complete. As expected, the genome of BU063 is more similar to Tannerella forsythia than any other known genome, although there are significant differences, including a 44% difference in gene content, changes in metabolic pathways, loss of synteny, and an 8-9% difference in GC content. Several identified virulence genes of T. forsythia are not found in BU063 including karilysin, prtH, and bspA. The absence of these genes may explain the lack of periodontal pathogenesis by this species and provides a new foundation to further understand the genome evolution and mechanisms of bacterial-host interaction in closely related oral microbes with different pathogenicity potential.

  5. Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

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    Shibaya Taeko

    2010-04-01

    Full Text Available Abstract Background To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition. Results The total 5.89-Gb sequence for Koshihikari, equivalent to 15.7× the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67 051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity Conclusions Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several

  6. No evidence of contemporary interploidy gene flow between the closely related European woodland violets Viola reichenbachiana and V. riviniana (sect. Viola, Violaceae).

    Science.gov (United States)

    Migdałek, G; Nowak, J; Saługa, M; Cieślak, E; Szczepaniak, M; Ronikier, M; Marcussen, T; Słomka, A; Kuta, E

    2017-07-01

    Viola reichenbachiana (2n = 4x = 20) and V. riviniana (2n = 8x = 40) are closely related species widely distributed in Europe, often sharing the same habitat throughout their overlapping ranges. It has been suggested in numerous studies that their high intraspecific morphological variability and plasticity might have been further increased by interspecific hybridisation in contact zones, given the sympatry of the species and the incomplete sterility of their hybrid. The aims of this study were to: (i) confirm that V. reichenbachiana and V. riviniana have one 4x genome in common, and (ii) determine the impact of hybridisation and introgression on genetic variation of these two species in selected European populations. For our study, we used 31 Viola populations from four European countries, which were analysed using AFLP and sequencing of a variable plastid intergenic spacer, trnH-psbA. Our analysis revealed that V. reichenbachiana exhibited larger haplotype diversity, having three species-specific haplotypes versus one in V. riviniana. The relationships among haplotypes suggest transfer of common haplotypes into V. riviniana from both V. reichenbachiana and hypothetically the other, now extinct, parental species. AFLP analysis showed low overall genetic diversity of both species, with V. riviniana showing higher among-population diversity. None of the morphologically designated hybrid populations had additive AFLP polymorphisms that would have indicated recent hybridisation. Also, kinship coefficients between both species did not indicate gene flow. V. riviniana showed significant population subdivision and significant isolation by distance, in contrast to V. reichenbachiana. The results indicate lack of gene flow between species, high influence of selfing on genetic variability, as well as probably only localised introgression toward V. riviniana. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

  7. Patient self-assessed shoulder comfort and function and active motion are not closely related to surgically documented rotator cuff tear integrity.

    Science.gov (United States)

    Hsu, Jason E; Tang, Anna; Matsen, Frederick A

    2017-07-06

    The rationale for rotator cuff repair surgery is that better integrity of the cuff should be associated with better comfort and function. However, in patients with cuff disease, there is not good evidence that the degree of rotator cuff integrity is closely associated with the shoulder's comfort, function, or active motion. The goal of this study was to explore these relationships in shoulders with surgically documented cuff disease. In 55 shoulders having surgery for cuff-related symptoms, we correlated the preoperative Simple Shoulder Test score with the objectively measured preoperative active shoulder motion and with the integrity of the cuff observed at surgery. The 16 shoulders with tendinosis or partial-thickness tears had an average Simple Shoulder Test score of 3.7 ± 3.3, active abduction of 111° ± 38°, and active flexion of 115° ± 36°. The corresponding values were 3.6 ± 2.8, 94° ± 47°, and 94° ± 52° for the 22 full-thickness supraspinatus tears and 3.9 ± 2.7, 89° ± 39°, and 100° ± 39° for the 17 supraspinatus and infraspinatus tears. In this study, surgically observed cuff integrity was not strongly associated with the shoulder's comfort or function. Whereas surgeons often seek to improve the integrity of the rotator cuff, the management of patients with rotator cuff disorders needs to be informed by a better understanding of the factors other than cuff integrity that influence the comfort and functioning of shoulders with cuff disease. Copyright © 2017 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

  8. A DNA barcoding method to discriminate between the model plant Brachypodium distachyon and its close relatives B. stacei and B. hybridum (Poaceae).

    Science.gov (United States)

    López-Alvarez, Diana; López-Herranz, Maria Luisa; Betekhtin, Alexander; Catalán, Pilar

    2012-01-01

    Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20) and their derived allotetraploid B. hybridum (2n = 30). We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF) and nuclear (ITS, GI) loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success) using direct trnLF (2.4%), ITS (5.5%) or GI (3.8%) sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success) or by cloned GI sequences (96.7%) that showed 5.4% (ITS) and 4% (GI) rate divergence between the two parental sequences found in the allopolyploid. Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents.

  9. 关注电磁学相关物理效应的教学%Paying Close Attention to Teaching of the Physical Effects Related to Electromagnetics

    Institute of Scientific and Technical Information of China (English)

    李长胜; 冯丽爽

    2015-01-01

    We propose to pay close attention to teaching of the physical effects related to electromagnetics in the courses of Theory of Electromagnetic Field and Electromagnetic Field&Wave,and analyze necessity and feasibility of the proposed teaching content. Teaching of electromagnetic effects is of great help to students to let them under-stand basic concepts and theorems of electromagnetic field and wave,to improve their innovation abilities,and to stimulate their interests of study and scientific research. Such factors as different students'majors,dependence on teaching content,and significance in theory and application,play great roles in the selection of electromagnetic effects to teach.%本文提出在“电磁场理论”和“电磁场与电磁波”课程教学中关注电磁学相关物理效应,并分析其必要性和可行性。关注电磁学效应的教学,将有助于学生对电磁场与电磁波相关基本概念和定理的理解,有利于提高学生的创新研究能力,有助于激发学生的学习兴趣和科研热情。在本课程教学过程中,可根据不同专业的需要和教学内容的相关性等,适当选讲具有一定理论和实际意义的电磁学效应。

  10. Three novel rice genes closely related to the Arabidopsis IRX9, IRX9L, and IRX14 genes and their roles in xylan biosynthesis

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    Dawn eChiniquy

    2013-04-01

    Full Text Available Xylan is the second most abundant polysaccharide on Earth, and represents a major component of both dicot wood and the cell walls of grasses. Much knowledge has been gained from studies of xylan biosynthesis in the model plant, Arabidopsis. In particular, the irregular xylem (irx mutants, named for their collapsed xylem cells, have been essential in gaining a greater understanding of the genes involved in xylan biosynthesis. In contrast, xylan biosynthesis in grass cell walls is poorly understood. We identified three rice genes Os07g49370 (OsIRX9, Os01g48440 (OsIRX9L, and Os06g47340 (OsIRX14, from glycosyltransferase family 43 as putative orthologs to the putative β-1,4-xylan backbone elongating Arabidopsis IRX9, IRX9L, and IRX14 genes, respectively. We demonstrate that the overexpression of the closely related rice genes, in full or partly complement the two well-characterized Arabidopsis irregular xylem (irx mutants: irx9 and irx14. Complementation was assessed by measuring dwarfed phenotypes, irregular xylem cells in stem cross sections, xylose content of stems, xylosyltransferase activity of stems, and stem strength. The expression of OsIRX9 in the irx9 mutant resulted in xylosyltransferase activity of stems that was over double that of wild type plants, and the stem strength of this line increased to 124% above that of wild type. Taken together, our results suggest that OsIRX9/OsIRX9L, and OsIRX14, have similar functions to the Arabidopsis IRX9 and IRX14 genes, respectively. Furthermore, our expression data indicate that OsIRX9 and OsIRX9L may function in building the xylan backbone in the secondary and primary cell walls, respectively. Our results provide insight into xylan biosynthesis in rice and how expression of a xylan synthesis gene may be modified to increase stem strength.

  11. Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow

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    Victor Borges Rezende

    2016-10-01

    Full Text Available Several fruit flies species of the Anastrepha fraterculus group are of great economic importance for the damage they cause to a variety of fleshy fruits. Some species in this group have diverged recently, with evidence of introgression, showing similar morphological attributes that render their identification difficult, reinforcing the relevance of identifying new molecular markers that may differentiate species. We investigated genes expressed in head tissues from two closely related species: A. obliqua and A. fraterculus, aiming to identify fixed single nucleotide polymorphisms (SNPs and highly differentiated transcripts, which, considering that these species still experience some level of gene flow, could indicate potential candidate genes involved in their differentiation process. We generated multiple libraries from head tissues of these two species, at different reproductive stages, for both sexes. Our analyses indicate that the de novo transcriptome assemblies are fairly complete. We also produced a hybrid assembly to map each species’ reads, and identified 67,470 SNPs in A. fraterculus, 39,252 in A. obliqua, and 6386 that were common to both species. We identified 164 highly differentiated unigenes that had a mean interspecific index (D¯ of at least 0.94. We selected unigenes that had Ka/Ks higher than 0.5, or had at least three or more highly differentiated SNPs as potential candidate genes for species differentiation. Among these candidates, we identified proteases, regulators of redox homeostasis, and an odorant-binding protein (Obp99c, among other genes. The head transcriptomes described here enabled the identification of thousands of genes hitherto unavailable for these species, and generated a set of candidate genes that are potentially important to genetically identify species and understand the speciation process in the presence of gene flow of A. obliqua and A. fraterculus.

  12. A DNA barcoding method to discriminate between the model plant Brachypodium distachyon and its close relatives B. stacei and B. hybridum (Poaceae.

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    Diana López-Alvarez

    Full Text Available BACKGROUND: Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10 and B. stacei (2n = 20 and their derived allotetraploid B. hybridum (2n = 30. METHODOLOGY/PRINCIPAL FINDINGS: We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF and nuclear (ITS, GI loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success using direct trnLF (2.4%, ITS (5.5% or GI (3.8% sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success or by cloned GI sequences (96.7% that showed 5.4% (ITS and 4% (GI rate divergence between the two parental sequences found in the allopolyploid. CONCLUSION/SIGNIFICANCE: Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents.

  13. Advantageous Direct Quantification of Viable Closely Related Probiotics in Petit-Suisse Cheeses under In Vitro Gastrointestinal Conditions by Propidium Monoazide - qPCR

    Science.gov (United States)

    Villarreal, Martha Lissete Morales; Padilha, Marina; Vieira, Antonio Diogo Silva; Franco, Bernadette Dora Gombossy de Melo; Martinez, Rafael Chacon Ruiz; Saad, Susana Marta Isay

    2013-01-01

    Species-specific Quantitative Real Time PCR (qPCR) alone and combined with the use of propidium monoazide (PMA) were used along with the plate count method to evaluate the survival of the probiotic strains Lactobacillus acidophilus La-5 and Bifidobacterium animalis subsp. lactis Bb-12, and the bacteriocinogenic and potentially probiotic strain Lactobacillus sakei subsp. sakei 2a in synbiotic (F1) and probiotic (F2) petit-suisse cheeses exposed throughout shelf-life to in vitro simulated gastrointestinal tract conditions. The three strains studied showed a reduction in their viability after the 6 h assay. Bb-12 displayed the highest survival capacity, above 72.6 and 74.6% of the initial populations, respectively, by plate count and PMA-qPCR, maintaining population levels in the range or above 6 log CFU/g. The prebiotic mix of inulin and FOS did not offer any additional protection for the strains against the simulated gastrointestinal environment. The microorganisms' populations were comparable among the three methods at the initial time of the assay, confirming the presence of mainly viable and culturable cells. However, with the intensification of the stress induced throughout the various stages of the in vitro test, the differences among the methods increased. The qPCR was not a reliable enumeration method for the quantification of intact bacterial populations, mixed with large numbers of injured and dead bacteria, as confirmed by the scanning electron microscopy results. Furthermore, bacteria plate counts were much lower (P<0.05) than with the PMA-qPCR method, suggesting the accumulation of stressed or dead microorganisms unable to form colonies. The use of PMA overcame the qPCR inability to differentiate between dead and alive cells. The combination of PMA and species-specific qPCR in this study allowed a quick and unequivocal way of enumeration of viable closely related species incorporated into probiotic and synbiotic petit-suisse cheeses and under stress

  14. Advantageous direct quantification of viable closely related probiotics in petit-suisse cheeses under in vitro gastrointestinal conditions by Propidium Monoazide--qPCR.

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    Martha Lissete Morales Villarreal

    Full Text Available Species-specific Quantitative Real Time PCR (qPCR alone and combined with the use of propidium monoazide (PMA were used along with the plate count method to evaluate the survival of the probiotic strains Lactobacillus acidophilus La-5 and Bifidobacterium animalis subsp. lactis Bb-12, and the bacteriocinogenic and potentially probiotic strain Lactobacillus sakei subsp. sakei 2a in synbiotic (F1 and probiotic (F2 petit-suisse cheeses exposed throughout shelf-life to in vitro simulated gastrointestinal tract conditions. The three strains studied showed a reduction in their viability after the 6 h assay. Bb-12 displayed the highest survival capacity, above 72.6 and 74.6% of the initial populations, respectively, by plate count and PMA-qPCR, maintaining population levels in the range or above 6 log CFU/g. The prebiotic mix of inulin and FOS did not offer any additional protection for the strains against the simulated gastrointestinal environment. The microorganisms' populations were comparable among the three methods at the initial time of the assay, confirming the presence of mainly viable and culturable cells. However, with the intensification of the stress induced throughout the various stages of the in vitro test, the differences among the methods increased. The qPCR was not a reliable enumeration method for the quantification of intact bacterial populations, mixed with large numbers of injured and dead bacteria, as confirmed by the scanning electron microscopy results. Furthermore, bacteria plate counts were much lower (P<0.05 than with the PMA-qPCR method, suggesting the accumulation of stressed or dead microorganisms unable to form colonies. The use of PMA overcame the qPCR inability to differentiate between dead and alive cells. The combination of PMA and species-specific qPCR in this study allowed a quick and unequivocal way of enumeration of viable closely related species incorporated into probiotic and synbiotic petit-suisse cheeses and

  15. Airflow limitation or static hyperinflation: which is more closely related to dyspnea with activities of daily living in patients with COPD?

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    Nishimura Takashi

    2011-10-01

    Full Text Available Abstract Background Dyspnea while performing the activities of daily living has been suggested to be a better measurement than peak dyspnea during exercise. Furthermore, the inspiratory capacity (IC has been shown to be more closely related to exercise tolerance and dyspnea than the FEV1, because dynamic hyperinflation is the main cause of shortness of breath in patients with COPD. However, breathlessness during exercise is measured in most studies to evaluate this relationship. Purpose To evaluate the correlation between breathlessness during daily activities and airflow limitation or static hyperinflation in COPD. Methods We examined 167 consecutive outpatients with stable COPD. The Baseline Dyspnea Index (BDI was used to evaluate dyspnea with activities of daily living. The relationship between the BDI score and the clinical measurements of pulmonary function was then investigated. Results The Spearman rank correlation coefficients (Rs between the BDI score and the FEV1(L, FEV1(%pred and FEV1/FVC were 0.60, 0.56 and 0.56, respectively. On the other hand, the BDI score also correlated with the IC, IC/predicted total lung capacity (TLC and IC/TLC (Rs = 0.45, 0.46 and 0.47, respectively. Although all of the relationships studied were strongly correlated, the correlation coefficients were better between dyspnea and airflow limitation than between dyspnea and static hyperinflation. In stepwise multiple regression analyses, the BDI score was most significantly explained by the FEV1 (R2 = 26.2% and the diffusion capacity for carbon monoxide (R2 = 14.4% (Cumulative R2 = 40.6%. Static hyperinflation was not a significant factor for clinical dyspnea on the stepwise multiple regression analysis. Conclusion Both static hyperinflation and airflow limitation contributed greatly to dyspnea in COPD patients.

  16. Visceral fat dominant distribution in male type 2 diabetic patients is closely related to hepatic insulin resistance, irrespective of body type

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    Miyazaki Yoshinori

    2009-08-01

    Full Text Available Abstract Background All previous studies that investigated the association between abdominal fat distribution and insulin resistance evaluated subcutaneous and visceral fat area and/or volume, but these values were not related to the body type of each subject. In the present study we have examined the association between abdominal fat distribution and peripheral (muscle/hepatic sensitivity to insulin using the visceral to abdominal subcutaneous fat area ratio (VF/SF ratio in male patients with type 2 diabetes mellitus. This ratio defines the predominancy of visceral or subcutaneous abdominal adiposity, independent of the body type of each individual. Methods Thirty-six type 2 diabetic male patients underwent a euglycemic insulin clamp (insulin infusion rate = 40 mU/m2·min with 3-3H-glucose to measure insulin-mediated total body (primarily reflects muscle glucose disposal (TGD and suppression of endogenous (primarily reflects liver glucose production (EGP in response to a physiologic increase in plasma insulin concentration. Abdominal subcutaneous (SF and intraabdominal visceral fat (VF areas were quantitated with magnetic resonance imaging (MRI at the level of L4–5. Results TGD and TGD divided by steady state plasma insulin concentration during the insulin clamp (TGD/SSPI correlated inversely with body mass index (BMI, total fat mass (FM measured by 3H2O, SF and VF areas, while VF/SF ratio displayed no significant relationship with TGD or TGD/SSPI. In contrast, EGP and the product of EGP and SSPI during the insulin clamp (an index hepatic insulin resistance correlated positively with VF/SF ratio, but not with BMI, FM, VF or SF. Conclusion We conclude that, independent of the individual's body type, visceral fat dominant accumulation as opposed to subcutaneous fat accumulation is associated with hepatic insulin resistance, whereas peripheral (muscle insulin resistance is more closely related to general obesity (i.e. higher BMI and total FM

  17. Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization

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    Harrison Marcus

    2010-12-01

    Full Text Available Abstract Background Whilst being closely related to the model actinomycete Streptomyces coelicolor A3(2, S. lividans 66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Previous comparative gene hybridization studies investigating such differences have used low-density (one probe per gene PCR-based spotted arrays. Here we use new experimentally optimised 104,000 × 60-mer probe arrays to characterize in detail the genomic differences between wild-type S. lividans 66, a derivative industrial strain, TK24, and S. coelicolor M145. Results The high coverage and specificity (detection of three nucleotide differences of the new microarrays used has highlighted the macroscopic genomic differences between two S. lividans strains and S. coelicolor. In a series of case studies we have validated the microarray and have identified subtle changes in genomic structure which occur in the Asp-activating adenylation domains of CDA non-ribosomal peptide synthetase genes which provides evidence of gene shuffling between these domains. We also identify single nucleotide sequence inter-species differences which exist in the actinorhodin biosynthetic gene cluster. As the glyoxylate bypass is non-functional in both S. lividans strains due to the absence of the gene encoding isocitrate lyase it is likely that the ethylmalonyl-CoA pathway functions as the alternative mechanism for the assimilation of C2 compounds. Conclusions This study provides evidence for widespread genetic recombination, rather than it being focussed at 'hotspots', suggesting that the previously proposed 'archipelago model' of genomic differences between S. coelicolor and S. lividans is unduly simplistic. The two S. lividans strains investigated differ considerably in genetic complement, with TK24 lacking 175 more genes than its wild-type parent when compared to S. coelicolor. Additionally, we confirm the presence of bldB in S. lividans and

  18. Temporomandibular Joint, Closed

    Science.gov (United States)

    ... Gallery > Oral Health > The Temporomandibular Joint, Closed The Temporomandibular Joint, Closed Main Content Title: The Temporomandibular Joint, Closed Description: The temporomandibular joint connects the lower ...

  19. Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

    Science.gov (United States)

    Tong, Chaobo; Guo, Baocheng; He, Shunping

    2009-01-01

    Background Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 × 105 and 1.7 × 105 per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened

  20. Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

    Directory of Open Access Journals (Sweden)

    Guo Baocheng

    2009-02-01

    Full Text Available Abstract Background Short and long interspersed elements (SINEs and LINEs, respectively, two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members, designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 × 105 and 1.7 × 105 per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp

  1. Differences in the mannose oligomer specificities of the closely related lectins from Galanthus nivalis and Zea mays strongly determine their eventual anti-HIV activity

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    Fouquaert Elke

    2011-02-01

    Full Text Available Abstract Background In a recent report, the carbohydrate-binding specificities of the plant lectins Galanthus nivalis (GNA and the closely related lectin from Zea mays (GNAmaize were determined by glycan array analysis and indicated that GNAmaize recognizes complex-type N-glycans whereas GNA has specificity towards high-mannose-type glycans. Both lectins are tetrameric proteins sharing 64% sequence similarity. Results GNAmaize appeared to be ~20- to 100-fold less inhibitory than GNA against HIV infection, syncytia formation between persistently HIV-1-infected HuT-78 cells and uninfected CD4+ T-lymphocyte SupT1 cells, HIV-1 capture by DC-SIGN and subsequent transmission of DC-SIGN-captured virions to uninfected CD4+ T-lymphocyte cells. In contrast to GNA, which preferentially selects for virus strains with deleted high-mannose-type glycans on gp120, prolonged exposure of HIV-1 to dose-escalating concentrations of GNAmaize selected for mutant virus strains in which one complex-type glycan of gp120 was deleted. Surface Plasmon Resonance (SPR analysis revealed that GNA and GNAmaize interact with HIV IIIB gp120 with affinity constants (KD of 0.33 nM and 34 nM, respectively. Whereas immobilized GNA specifically binds mannose oligomers, GNAmaize selectively binds complex-type GlcNAcβ1,2Man oligomers. Also, epitope mapping experiments revealed that GNA and the mannose-specific mAb 2G12 can independently bind from GNAmaize to gp120, whereas GNAmaize cannot efficiently bind to gp120 that contained prebound PHA-E (GlcNAcβ1,2man specific or SNA (NeuAcα2,6X specific. Conclusion The markedly reduced anti-HIV activity of GNAmaize compared to GNA can be explained by the profound shift in glycan recognition and the disappearance of carbohydrate-binding sites in GNAmaize that have high affinity for mannose oligomers. These findings underscore the need for mannose oligomer recognition of therapeutics to be endowed with anti-HIV activity and that mannose, but

  2. Comparative analysis of emm type pattern of Group A Streptococcus throat and skin isolates from India and their association with closely related SIC, a streptococcal virulence factor

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    Ganguly Nirmal K

    2008-09-01

    Full Text Available Abstract Background Group A streptococcus (GAS causes a wide variety of life threatening diseases in humans and the incidence of such infections is high in developing countries like India. Although distribution of emm types of GAS in India has been described, there is a lack of data describing either the comparative distribution of emm types in throat versus skin isolates, or the distribution of certain virulence factors amongst these isolates. Therefore in the present study we have monitored the emm type pattern of Group A streptococcus throat and skin isolates from India. Additionally, the association of these isolates with closely related sic (crs, a multifunctional compliment binding virulence factor, was also explored. Results Of the 94 (46 throat and 48 skin isolates analyzed, 37 emm types were identified. The most frequently observed emm types were emm49 (8.5% and emm112 (7.5% followed by 6.5% each of emm1-2, emm75, emm77, and emm81. Out of 37 emm types, 27 have been previously reported and rest were isolated for the first time in the Indian Community. The predominant emm types of throat (emm49 and emm75 samples were different from those of skin (emm44, emm81 and emm112 samples. After screening all the 94 isolates, the crs gene was found in six emm1-2 (crs1-2 isolates, which was confirmed by DNA sequencing and expression analysis. Despite the polymorphic nature of crs, no intravariation was observed within crs1-2. However, insertions and deletions of highly variable sizes were noticed in comparison to CRS isolated from other emm types (emm1.0, emm57. CRS1-2 showed maximum homology with CRS57, but the genomic location of crs1-2 was found to be the same as that of sic1.0. Further, among crs positive isolates, speA was only present in skin samples thus suggesting possible role of speA in tissue tropism. Conclusion Despite the diversity in emm type pattern of throat and skin isolates, no significant association between emm type and source of

  3. On the relation between the fundamental equation of thermodynamics and the energy balance equation in the context of closed and open systems

    NARCIS (Netherlands)

    Knuiman, J.T.; Barneveld, P.A.

    2012-01-01

    In this paper, we elaborate on the connection between the fundamental equation of thermodynamics, which is essentially the combination of the First and Second Laws of thermodynamics, and the energy balance equation in the context of closed and open systems. We point out some misinterpretations in

  4. On the relation between the fundamental equation of thermodynamics and the energy balance equation in the context of closed and open systems

    NARCIS (Netherlands)

    Knuiman, J.T.; Barneveld, P.A.

    2012-01-01

    In this paper, we elaborate on the connection between the fundamental equation of thermodynamics, which is essentially the combination of the First and Second Laws of thermodynamics, and the energy balance equation in the context of closed and open systems. We point out some misinterpretations in at

  5. Immunohistochemistry and molecular epidemiology of avian paramyxovirus 1 from formalin-fixed and paraffin-embedded sections of Japanese doves (Columba livia) affected with neurological signs.

    Science.gov (United States)

    Nakamura, Kikuyasu; Fujimori, Hideo; Koyama, Akiko; Dai, Trinh Quang; Imai, Kunitoshi; Ikezawa, Mitsutaka; Yamamoto, Yu

    2015-07-01

    Four doves (Nos. 1-4 birds) affected with neurological signs (ataxia, circling and torticollis) were investigated pathologically and microbiologically. Viral isolation was tried from the tracheal and cloacal swabs of all 4 birds and from liver, spleen, kidney, heart, lung and brain of Nos. 1 and 2 birds. No viruses were isolated from 4 birds, but they had high serum antibody titers against avian paramyxovirus 1 (APMV-1). Histologically, they had the characteristic histological changes of pigeon APMV-1 infection; nonpurulent encephalitis and interstitial nephritis. Immununohistochemically, APMV-1 antigens were detected in the necrotic renal tubular epithelial cells of 1 bird of them (No. 3 bird). Detection of APMV-1 ribonucleic acid (RNA) from formalin-fixed and paraffin-embedded (FFPE) sections was attempted by reverse transcription-polymerase chain reaction (RT-PCR). Sequencing the RT-PCR product showed the virus RNA belonged to the same APMV-1 genotype (VI) as the strains isolated from the world previous cases of pigeon APMV-1 infection. The RT-PCR of FFPE sections and sequencing of RT-PCR products are useful for molecular epidemiology of the virus when viral isolation from fresh samples is unsuccessful.

  6. Screening of Feral Pigeon (Colomba livia, Mallard (Anas platyrhynchos and Graylag Goose (Anser anser Populations for Campylobacter spp., Salmonella spp., Avian Influenza Virus and Avian Paramyxovirus

    Directory of Open Access Journals (Sweden)

    Nesse LL

    2005-12-01

    Full Text Available A total of 119 fresh faecal samples were collected from graylag geese migrating northwards in April. Also, cloacal swabs were taken from 100 carcasses of graylag geese shot during the hunting season in August. In addition, samples were taken from 200 feral pigeons and five mallards. The cultivation of bacteria detected Campylobacter jejuni jejuni in six of the pigeons, and in one of the mallards. Salmonella diarizona 14:k:z53 was detected in one graylag goose, while all pigeons and mallards were negative for salmonellae. No avian paramyxovirus was found in any of the samples tested. One mallard, from an Oslo river, was influenza A virus positive, confirmed by RT-PCR and by inoculation of embryonated eggs. The isolate termed A/Duck/Norway/1/03 was found to be of H3N8 type based on sequence analyses of the hemagglutinin and neuraminidase segments, and serological tests. This is the first time an avian influenza virus has been isolated in Norway. The study demonstrates that the wild bird species examined may constitute a reservoir for important bird pathogens and zoonotic agents in Norway.

  7. Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America.

    Science.gov (United States)

    Ramey, Andrew M; Goraichuk, Iryna V; Hicks, Joseph T; Dimitrov, Kiril M; Poulson, Rebecca L; Stallknecht, David E; Bahl, Justin; Afonso, Claudio L

    2017-03-03

    Avian paramyxovirus serotype 1 (APMV-1) viruses are globally distributed, infect wild, peridomestic, and domestic birds, and sometimes lead to outbreaks of disease. Thus, the maintenance, evolution, and spread of APMV-1 viruses are relevant to avian health. In this study we sequenced the fusion gene from 58 APMV-1 isolates recovered from thirteen species of wild birds sampled throughout the USA during 2007-2014. We analyzed sequence information with previously reported data in order to assess contemporary genetic diversity and inter-taxa/inter-region exchange of APMV-1 in wild birds sampled in North America. Our results suggest that wild birds maintain previously undescribed genetic diversity of APMV-1; however, such diversity is unlikely to be pathogenic to domestic poultry. Phylogenetic analyses revealed that APMV-1 diversity detected in wild birds of North America has been found in birds belonging to numerous taxonomic host orders and within hosts inhabiting multiple geographic regions suggesting some level of viral exchange. However, our results also provide statistical support for associations between phylogenetic tree topology and host taxonomic order/region of sample origin which supports restricted exchange among taxa and geographical regions of North America for some APMV-1 sub-genotypes. We identify previously unrecognized genetic diversity of APMV-1 in wild birds in North America which is likely a function of continued viral evolution in reservoir hosts. We did not, however, find support for the emergence or maintenance of APMV-1 strains predicted to be pathogenic to poultry in wild birds of North America outside of the order Suliformes (i.e., cormorants). Furthermore, genetic evidence suggests that ecological drivers or other mechanisms may restrict viral exchange among taxa and regions of North America. Additional and more systematic sampling for APMV-1 in North America would likely provide further inference on viral dynamics for this infectious agent

  8. Down-regulation of paramyxovirus hemagglutinin-neuraminidase glycoprotein surface expression by a mutant fusion protein containing a retention signal for the endoplasmic reticulum.

    Science.gov (United States)

    Tanaka, Y; Heminway, B R; Galinski, M S

    1996-08-01

    The human parainfluenza virus type 3 (HPIV3) fusion (F) and hemagglutinin-neuraminidase (HN) glycoproteins are the principal components involved in virion receptor binding, membrane penetration, and ultimately, syncytium formation. While the requirement for both F and HN in this process has been determined from recombinant expression studies, stable physical association of these proteins in coimmunoprecipitation studies has not been observed. In addition, coexpression of other heterologous paramyxovirus F or HN glycoproteins with either HPIV3 F or HN does not result in the formation of syncytia, suggesting serotype-specific protein differences. In this study, we report that simian virus 5 and Sendai virus heterologous HN proteins and measles virus hemagglutinin (H) were found to be down-regulated when coexpressed with HPIV3 F. As an alternative to detecting physical associations of these proteins by coimmunoprecipitation, further studies were performed with a mutant HPIV3 F protein (F-KDEL) lacking a transmembrane anchor and cytoplasmic tail and containing a carboxyl-terminal retention signal for the endoplasmic reticulum (ER). F-KDEL was defective for transport to the cell surface and could down-regulate surface expression of HPIV3 HN and heterologous HN/H proteins from simian virus 5, Sendai virus, and measles virus in coexpression experiments. HN/H down-regulation appeared to result, in part, from an early block to HPIV3 HN synthesis, as well as an instability of the heterologous HN/H proteins within the ER. In contrast, coexpression of F-KDEL with HPIV3 wild-type F or the heterologous receptor-binding proteins, respiratory syncytial virus glycoprotein (G) and vesicular stomatitis virus glycoprotein (G), were not affected in transport to the cell surface. Together, these results support the notion that the reported serotype-specific restriction of syncytium formation may involve, in part, down-regulation of heterologous HN expression.

  9. The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well-studied model organism, Escherichia coli-K12.

    Science.gov (United States)

    Vijayendran, Chandran; Polen, Tino; Wendisch, Volker F; Friehs, Karl; Niehaus, Karsten; Flaschel, Erwin

    2007-03-10

    The use of Escherichia coli as a model organism has provided a great deal of basic information in biomolecular sciences. Examining trait differences among closely related strains of the same species addresses a fundamental biological question: how much diversity is there at the single species level? The main aim of our research was to identify significant differences in the activities of groups of genes between two laboratory strains of an organism closely related in genome structure. We demonstrate that despite strict and controlled growth conditions, there is high plasticity in the global proteome and genome expression in two closely related E. coli K12 sub-strains (W3110 and MG1655), which differ insignificantly in genome structure. The growth patterns of these two sub-strains were very similar in a well-equipped bioreactor, and their genome structures were shown to be almost identical by DNA microarray. However, detailed profiling of protein and gene expression by 2-dimensional gel electrophoresis and microarray analysis showed many differentially expressed genes and proteins, combinations of which were highly correlated. The differentially regulated genes and proteins belonged to the following functional categories: genes regulated by sigma subunit of RNA polymerase (RpoS), enterobactin-related genes, and genes involved in central metabolism. Genes involved in central cell metabolism - the glycolysis pathway, the tricarboxylic acid cycle and the glyoxylate bypass - were differentially regulated at both the mRNA and proteome levels. The strains differ significantly in central metabolism and thus in the generation of precursor metabolites and energy. This high plasticity probably represents a universal feature of metabolic activities in closely related species, and has the potential to reveal differences in regulatory networks. We suggest that unless care is taken in the choice of strains for any validating experiment, the results might be misleading.

  10. Comprehensive Serology Based on a Peptide ELISA to Assess the Prevalence of Closely Related Equine Herpesviruses in Zoo and Wild Animals.

    Directory of Open Access Journals (Sweden)

    Azza Abdelgawad

    Full Text Available Equine herpesvirus type 1 (EHV-1 causes respiratory disorders and abortion in equids while EHV-1 regularly causes equine herpesvirus myeloencephalopathy (EHM, a stroke-like syndrome following endothelial cell infection in horses. Both EHV-1 and EHV-9 infections of non-definitive hosts often result in neuronal infection and high case fatality rates. Hence, EHV-1 and EHV-9 are somewhat unusual herpesviruses and lack strict host specificity, and the true extent of their host ranges have remained unclear. In order to determine the seroprevalence of EHV-1 and EHV-9, a sensitive and specific peptide-based ELISA was developed and applied to 428 sera from captive and wild animals representing 30 species in 12 families and five orders. Members of the Equidae, Rhinocerotidae and Bovidae were serologically positive for EHV-1 and EHV-9. The prevalence of EHV-1 in the sampled wild zebra populations was significantly higher than in zoos suggesting captivity may reduce exposure to EHV-1. Furthermore, the seroprevalence for EHV-1 was significantly higher than for EHV-9 in zebras. In contrast, EHV-9 antibody prevalence was high in captive and wild African rhinoceros species suggesting that they may serve as a reservoir or natural host for EHV-9. Thus, EHV-1 and EHV-9 have a broad host range favoring African herbivores and may have acquired novel natural hosts in ecosystems where wild equids are common and are in close contact with other perissodactyls.

  11. The solution properties of mefenamic acid and a closely related analogue are indistinguishable in polar solvents but significantly different in nonpolar environments.

    Science.gov (United States)

    Lee, Eun Hee; Byrn, Stephen R; Pinal, Rodolfo

    2012-12-01

    This study investigates the cosolute effects of mefenamic acid (XA) and flufenamic acid (FA). These compounds serve as model of a drug discovery lead compound and a structural analogue. The activity coefficients of XA and FA in different solvents were obtained from solubility measurements at 25°C. The effect of varying concentrations of FA on the solubility of XA in four different solvents, including toluene, cyclohexane, ethanol, and an ethanol-water mixture (80:20, v/v), was investigated. The magnitude of change in the activity coefficient of XA in the presence of FA in different solvents was used to elucidate the thermodynamic effect of FA on the solubility of XA. Nuclear magnetic resonance and Fourier-transform infrared spectroscopy were used to obtain molecular level information about the interactions of the compounds in solution. The presence of FA increases XA solubility in toluene and in cyclohexane as much as seven-fold. Conversely, in ethanol and the ethanol-water mixture, similar levels of FA have essentially no effect on the solubility of XA. The solution properties investigated show that despite the close structural similarity between XA and FA, the two compounds are strongly distinguishable in nonpolar solvents. Conversely, the solution properties of the same two solutes are indistinguishable in polar solvents. A solubilization model based on solute-cosolute interactions is presented.

  12. Association of Hepatitis B Virus Covalently Closed Circular DNA and Human APOBEC3B in Hepatitis B Virus-Related Hepatocellular Carcinoma.

    Directory of Open Access Journals (Sweden)

    Xuan Luo

    Full Text Available Chronic Hepatitis B Virus (HBV infections can progresses to liver cirrhosis and hepatocellular carcinoma (HCC. The HBV covalently-closed circular DNA cccDNA is a key to HBV persistence, and its degradation can be induced by the cellular deaminase APOBEC3. This study aimed to measure the distribution of intrahepatic cccDNA levels and evaluate the association between levels of cccDNA and APOBEC3 in HCC patients. Among 49 HCC patients, 35 matched cancerous and contiguous noncancerous liver tissues had detectable cccDNA, and the median intrahepatic cccDNA in the cancerous tissues (CT was significantly lower than in the contiguous noncancerous tissues (CNCT (p = 0.0033. RCA (rolling circle amplification, followed by 3D-PCR identified positive amplification in 27 matched HCC patients. Sequence analysis indicated G to A mutations accumulated to higher levels in CT samples compared to CNCT samples, and the dinucleotide context showed preferred editing in the GpA context. Among 7 APOBEC3 genes, APOBEC3B was the only one up-regulated in cancerous tissues both at the transcriptional and protein levels (p < 0.05. This implies APOBEC3B may contribute to cccDNA editing and subsequent degradation in cancerous tissues.

  13. Identification and characterization of miRNAs in two closely related C4 and C3 species of Cleome by high-throughput sequencing

    Science.gov (United States)

    Gao, Shuangcheng; Zhao, Wei; Li, Xiang; You, Qingbo; Shen, Xinjie; Guo, Wei; Wang, Shihua; Shi, Guoan; Liu, Zheng; Jiao, Yongqing

    2017-04-01

    Cleome gynandra and Cleome hassleriana, which are C4 and C3 plants, respectively, are two species of Cleome. The close genetic relationship between C. gynandra and C. hassleriana provides advantages for discovering the differences in leaf development and physiological processes between C3 and C4 plants. MicroRNAs (miRNAs) are a class of important regulators of various biological processes. In this study, we investigate the differences in the characteristics of miRNAs between C. gynandra and C. hassleriana using high-throughput sequencing technology. In total, 94 and 102 known miRNAs were identified in C. gynandra and C. hassleriana, respectively, of which 3 were specific for C. gynandra and 10 were specific for C. hassleriana. Ninety-one common miRNAs were identified in both species. In addition, 4 novel miRNAs were detected, including three in C. gynandra and three in C. hassleriana. Of these miRNAs, 67 were significantly differentially expressed between these two species and were involved in extensive biological processes, such as glycol-metabolism and photosynthesis. Our study not only provided resources for C. gynandra and C. hassleriana research but also provided useful clues for the understanding of the roles of miRNAs in the alterations of biological processes in leaf tissues during the evolution of the C4 pathway.

  14. Türk Edebiyatında Birbirine Yakın Üç Kelime: Hiciv, Medih ve Hezel
    Three Closely Related Concepts in Turkish Literature: Satire, Eulogy, and Comic Poem

    OpenAIRE

    Zülküf KILIÇ

    2012-01-01

    About social criticism in literature, it has been determined that ancient poets and authors used lots of words and concepts, but it is clear that especially the concepts like satire, comic poem and eulogy were widely used for the literature which deals mainly with the personal, objective and the social criticism. Lots of other concepts which are related to the subject are synonymous have a close meaning with these, and they are expressed collectively under the main title of satire. First, we ...

  15. Comparing two levels of closed system suction pressure in ICU patients: Evaluating the relative safety of higher values of suction pressure.

    Science.gov (United States)

    Yazdannik, Ahmad R; Haghighat, Somayeh; Saghaei, Mahmoud; Eghbali, Maryam

    2013-03-01

    Endotracheal suctioning (ETS) is one of the most common supportive measures in intensive care units (ICU). ETS may be associated with complications including hypoxia and tachycardia. Closed system suctioning (CSS) decreases the rate of cardiorespiratory complication mainly due to continuation of ventilatory support and oxygenation during procedure. CSS has questionable efficacy, therefore higher values of negative pressure has been recommended to enhance the efficacy of CSS. This study was designed to evaluate the effects on gas exchange of 200 mmHg suctioning pressure compared with 100 mmHg in CSS. Fifty mechanically ventilated (MV) ICU patients were selected for the study. Two consecutive ten seconds CSS using suction pressures of 100 and 200 mmHg, in random order applied in each subject with the two hours wash out period. Effects of two levels of suction pressure on gas exchange were measured by recording the SPo2 values at 4 times. Repeated measure analysis of variance didn't show any significant difference between two levels of pressure (P = 0.315), but within each groups (100 and 200 mmHg) SPO2 changes was significant (P = 0.000). There was a mild but significant and transient increase in heart rate following both suction pressures, but no significant difference between two groups. The results show that CSS with suction pressure 200 mmHg has no detrimental effect on cardiorespiratory function of MV ICU patients. Since the safety of 200 mmHg suctioning pressure was approved, using 200 mmHg suction pressures is recommended for ETS of MV patients.

  16. Comparing two levels of closed system suction pressure in ICU patients: Evaluating the relative safety of higher values of suction pressure

    Science.gov (United States)

    Yazdannik, Ahmad R.; Haghighat, Somayeh; Saghaei, Mahmoud; Eghbali, Maryam

    2013-01-01

    Background: Endotracheal suctioning (ETS) is one of the most common supportive measures in intensive care units (ICU). ETS may be associated with complications including hypoxia and tachycardia. Closed system suctioning (CSS) decreases the rate of cardiorespiratory complication mainly due to continuation of ventilatory support and oxygenation during procedure. CSS has questionable efficacy, therefore higher values of negative pressure has been recommended to enhance the efficacy of CSS. This study was designed to evaluate the effects on gas exchange of 200 mmHg suctioning pressure compared with 100 mmHg in CSS. Materials and Methods: Fifty mechanically ventilated (MV) ICU patients were selected for the study. Two consecutive ten seconds CSS using suction pressures of 100 and 200 mmHg, in random order applied in each subject with the two hours wash out period. Effects of two levels of suction pressure on gas exchange were measured by recording the SPo2 values at 4 times. Results: Repeated measure analysis of variance didn't show any significant difference between two levels of pressure (P = 0.315), but within each groups (100 and 200 mmHg) SPO2 changes was significant (P = 0.000). There was a mild but significant and transient increase in heart rate following both suction pressures, but no significant difference between two groups. Conclusion: The results show that CSS with suction pressure 200 mmHg has no detrimental effect on cardiorespiratory function of MV ICU patients. Since the safety of 200 mmHg suctioning pressure was approved, using 200 mmHg suction pressures is recommended for ETS of MV patients. PMID:23983740

  17. The close relation between Lactococcus and Methanosaeta is a keystone for stable methane production from molasses wastewater in a UASB reactor.

    Science.gov (United States)

    Kim, Tae Gwan; Yun, Jeonghee; Cho, Kyung-Suk

    2015-10-01

    The up-flow anaerobic sludge blanket (UASB) reactor is a promising method for the treatment of high-strength industrial wastewaters due to advantage of its high treatment capacity and settleable suspended biomass retention. Molasses wastewater as a sugar-rich waste is one of the most valuable raw material for bioenergy production due to its high organic strength and bioavailability. Interpretation for complex interactions of microbial community structures and operational parameters can help to establish stable biogas production. RNA-based approach for biogas production systems is recommended for analysis of functionally active community members which are significantly underestimated. In this study, methane production and active microbial community were characterized in an UASB reactor using molasses wastewater as feedstock. The UASB reactor achieved a stable process performance at an organic loading rate of 1.7~13.8-g chemical oxygen demand (COD,·L(-1) day(-1); 87-95 % COD removal efficiencies), and the maximum methane production rate was 4.01 L-CH4·at 13.8 g-COD L(-1) day(-1). Lactococcus and Methanosaeta were comprised up to 84 and 80 % of the active bacterial and archaeal communities, respectively. Network analysis of reactor performance and microbial community revealed that Lactococcus and Methanosaeta were network hub nodes and positively correlated each other. In addition, they were positively correlated with methane production and organic loading rate, and they shared the other microbial hub nodes as neighbors. The results indicate that the close association between Lactococcus and Methanosaeta is responsible for the stable production of methane in the UASB reactor using molasses wastewater.

  18. Onion thrips, Thrips tabaci, have gut bacteria that are closely related to the symbionts of the western flower thrips, Frankliniella occidentalis

    NARCIS (Netherlands)

    Vries, de E.J.; Wurff, van der A.W.G.; Jacobs, G.; Breeuwer, J.A.J.

    2008-01-01

    It has been shown that many insects have Enterobacteriaceae bacteria in their gut system. The western flower thrips, Frankliniella occidentalis Pergande [Thysanoptera: Thripidae], has a symbiotic relation with Erwinia species gut bacteria. To determine if other Thripidae species have similar bacteri

  19. 鸽副黏病毒油乳剂灭活疫苗不同水油比的研究%Study on the pigeon paramyxovirus inactivated vaccine of different water?oil ratio

    Institute of Scientific and Technical Information of China (English)

    蒋凤英; 张俊平; 何锡忠; 张春玲; 李春华; 周宗清; 杨惠萍; 倪建平

    2015-01-01

    为了减少鸽副黏病毒油乳剂灭活疫苗的副作用,保证疫苗的安全性及免疫效果,利用分离到的鸽Ⅰ型副黏病毒(S-1株)作为抗原,配制了不同水油比的疫苗,对疫苗的物理性状、安全性、效力试验及免疫效果进行观察,探究疫苗不同水油比的差异。结果表明:该疫苗的水油乳化比为1∶4时,疫苗的稳定性最好、免疫效果最佳。%In order to reduce the side-effects of pigeon paramyxovirus oil emulsion inactivated vaccine and ensure the safety and immune effect of vaccine,the isolated pigeon paramyxovirus S-1 strain was used as the anti-gen to prepare with different water?oil ratio.The physical characteristics,safety,efficacy and immune effect of the vaccine were observed to explore the vaccine differences of different water?oil ratio.The results indicated that the vaccine has the best stability and immune effect when the water?oil ratio is 1∶4.

  20. Empirical L-M, R-M, and M-Teff relations for main-sequence stars: Components of close binary systems and low-mass stars

    Science.gov (United States)

    Gorda, S. Yu.; Svechnikov, M. A.

    1999-08-01

    A new catalog of photometric, geometric, and absolute elements of 112 detached main-sequence eclipsing variables with known photometric and spectroscopic orbital elements has been combined with speckle-interferometry data for low-mass stars to yield new mass-luminosity, mass-radius, and mass-spectrum relations: M_bol = 4.46 - 9.52 - (lg M > -0.4), M_bol = 6.18 - 5.91 lg M (lg M 0.14), lg R = 0.10 + 1.03 lg M (lg M 3.6), and lg M = - 29.4 + 8.2 lg T_eff (lg T_eff masses and radii used are accurate to 2-3 and 2-4%, respectively; the errors for low-mass stars are larger by factors of 3-4. The coefficients in the relations were derived using linear least squares fitting with corrections for noise in the independent variable.

  1. Molecular Survey of Anaplasma Species in Small Ruminants Reveals the Presence of Novel Strains Closely Related to A. phagocytophilum in Tunisia.

    Science.gov (United States)

    Ben Said, Mourad; Belkahia, Hanène; Alberti, Alberto; Zobba, Rosanna; Bousrih, Maha; Yahiaoui, Mouna; Daaloul-Jedidi, Monia; Mamlouk, Aymen; Gharbi, Mohamed; Messadi, Lilia

    2015-10-01

    A survey of Anaplasma species in small ruminants is still lacking in North African countries. In this study, the presence of A. phagocytophilum, A. phagocytophilum-related species, and A. ovis was investigated in a total of 563 healthy small ruminants (303 goats and 260 sheep), from 25 randomly selected flocks sampled in Tunisia. Anaplasma spp. and A. ovis overall infection rates were 95.0% and 93.8% in sheep and 69.6% and 65.3% in goats, respectively. A. phagocytophilum was not detected in any of tested animals. A total of 20 sheep (7.7%) and 144 goats (47.5%) were infected by Anaplasma strains genetically related to A. phagocytophilum. Both in sheep and goats A. ovis prevalence was higher in adults (≥2 years) than in young (<2 years) subjects (p = 0.001 and 0.002 for goats and sheep, respectively). In sheep, A. ovis prevalence was higher in ewes with respect to rams (p = 0.010). The A. ovis infection rate was significantly lower in goats of the local breed (p = 0.049) and it was higher in goats infested by ticks than in not infested animals (p = 0.005). Genetic analysis of the msp4 gene of A. ovis indicated the presence of strains shared by Tunisian sheep and goats. Sequence analysis and phylogenetic studies on the basis of the 16S rRNA gene provided evidence for the circulation of at least two different potentially novel species genetically related to A. phagocytophilum in Tunisian small ruminants. These findings cause concern about specificity of serological tests used for detection of A. phagocytophilum in ruminants and provide additional information for elucidating pathogenesis and molecular epidemiology of A. phagocytophilum and related species.

  2. Live music therapy in waiting area of intensive care units: a novel concept for betterment of close relatives of ICU patients

    Directory of Open Access Journals (Sweden)

    Sundar Sumathy

    2016-03-01

    Full Text Available Family members of ICU patients experience high levels of stress and anxiety. We explored a novel concept of live music therapy for relatives of ICU patients. Weekly 1-hour sessions of live music therapy consisting of devotional songs and prayers were performed in waiting area of ICU in a tertiary care hospital. Responses of 100 first degree relatives of ICU patients were documented using an 8-item questionnaire. 69% of the subjects rated live music therapy sessions as and ldquo;excellent and rdquo;; 50% of the subjects reported that they felt and ldquo;excellent and rdquo; after a single session. Such sessions were reported as a felt need by 77% of the subjects; 92% of the subjects reported that there were high chances that they would recommend such sessions in the hospital in future. In our study, we found our concept to be feasible, acceptable and highly appreciated as well as encouraged by first degree relatives of ICU patients. [Int J Res Med Sci 2016; 4(3.000: 947-949

  3. Multiplicity of Galactic Cepheids from long-baseline interferometry~III. Sub-percent limits on the relative brightness of a close companion of $\\delta$~Cephei

    CERN Document Server

    Gallenne, A; Kervella, P; Monnier, J D; Schaefer, G H; Roettenbacher, R M; Gieren, W; Pietrzynski, G; McAlister, H; Brummelaar, T ten; Sturmann, J; Sturmann, L; Turner, N; Anderson, R I

    2016-01-01

    We report new CHARA/MIRC interferometric observations of the Cepheid archetype $\\delta$ Cep, which aimed at detecting the newly discovered spectroscopic companion. We reached a maximum dynamic range $\\Delta H $ = 6.4, 5.8, and 5.2 mag, respectively within the relative distance to the Cepheid $r 9.15, 8.31$ and 7.77 mag, respectively for $r < 25$ mas, $25 < r < 50$ mas and $50 < r < 100$ mas. We also found that to be consistent with the predicted orbital period, the companion has to be located at a projected separation $< 24$ mas with a spectral type later than a F0V star.

  4. HTF: A b-ZIP transcription factor that is closely related to the human XBP/TREB5 and is activated by hepatocellular carcinoma in rats.

    Science.gov (United States)

    Kishimoto, T; Kokura, K; Kumagai, Y; Wakamatsu, T; Makino, Y; Tamura, T

    1996-06-25

    We screened for rat hepatocellular carcinoma (HCC)-related genes by a novel cDNA subtraction method and obtained one gene. This gene was transcribed as 2.0- and 2.5-kb mRNAs, and its transcription was specifically enhanced in HCC. These cDNAs had the same open reading frame, but the 2.5 kb transcript had an extra 495 bases of 5'-UTR at the 5'-terminus. The deduced aa sequence revealed a basic-leucine zipper (b-ZIP) and proline/glutamine-rich structures, both of which are characteristic motifs for transcription factors. We designated the translation product of this gene HTF (Hepatocarcinogenesis-related Transcription Factor). Electrophoretic mobility shift assay demonstrated the DNA-binding ability of the recombinant HTF. It is most interesting that HTF had a considerable homology with human XBP/TREB5, which has been reported to be a binding factor for the X-box of the MHC class II gene and for the 21-bp enhancer of the HTLV-1 LTR. Genomic Southern analysis suggested that the 2.0- and 2.5-kb mRNAs are transcribed by a dual promoter of a single gene. Our results may suggest that HTF is a b-ZIP-type transcription factor involved in rat hepatocellular carcinoma.

  5. Geochemistry and petrogenesis of extension-related magmas close to the volcanic front of the central part of the Trans-Mexican Volcanic Belt

    Science.gov (United States)

    Verma, Surendra P.; Torres-Sánchez, Darío; Velasco-Tapia, Fernando; Subramanyam, K. S. V.; Manikyamba, C.; Bhutani, Rajneesh

    2016-12-01

    New geochemical data for 23 samples from the Sierra de Chichinautzin (SCN) and Sierra Santa Catarina (SSC) located at the volcanic front of the central part of the Trans-Mexican Volcanic Belt were combined with the published data on 580 samples from the SCN to explore the origin and evolution of the Quaternary trachybasalt and basalt to andesite and dacite. The rare-earth element concentrations for the evolved intermediate and acid rocks are lower than those for the more basic varieties, implying that the evolved magmas cannot be generated by a simple fractional crystallisation process without crustal assimilation. The size of the Nb and Ta negative anomalies increases from basic to acid, which is similar to the behaviour of most continental rifts and extension-related areas, but contrasts from all island and continental arcs. The multidimensional tectonomagmatic diagrams indicate a continental rift setting from basic and alkaline intermediate magmas. The SSC represents a new site of within-plate alkaline magmas discovered in this work, which complements the earlier interpretation of the adjacent SCN as a manifestation of continental rift or extension-related magmatism.

  6. Is anti-doping analysis so far from clinical, legal or forensic targets?: The added value of close relationships between related disciplines.

    Science.gov (United States)

    Segura, Jordi

    2009-11-01

    There are many areas of common interest between anti-doping laboratories and those working in the clinical, legal and forensic fields. In addition to methodological similarities, there are aspects of the findings in sport drug testing that overlap with other fields in such a way that sport drug testing and clinical, legal or forensic work may benefit from mutual interaction. Three recent examples are presented from the author's experience. Case report 1 concerns the clinical relevance of hCG findings in sport drug testing as potential indicators of the presence of a (testicular) tumour in athletes. Case report 2 refers to difficulties that accredited laboratories can encounter due to differences between national legal systems and the administrative regulation systems of sport authorities. The example involves a network of blood collection for further autologous transfusion. Case report 3 relates to additional forensic-type investigations needed to interpret a situation where intoxication of a whole delegation was responsible for apparent doping cases. Clinical, legal and forensic fields must recognize the added value that some results and developments coming from anti-doping laboratories may have. At the same time anti-doping analysts should be aware of new issues, methodologies and problems appearing in related fields.

  7. Systematic study of favored \\alpha-decay half-lives of closed shell odd-A and doubly-odd nuclei related to ground and isomeric states

    CERN Document Server

    Sun, Xiao-Dong; Li, Xiao-Hua

    2016-01-01

    In this work, we systematically investigate the favored $\\alpha$-decay half-lives and $\\alpha$ preformation probabilities of both odd-$A$ and doubly-odd nuclei related to ground and isomeric states around the doubly magic cores at $Z=82$, $N=82$ and at $Z=82$, $N=126$, respectively, within a two-potential approach from the view of the valence nucleon (or hole). The results show that the $\\alpha$ preformation probability is linear related to $N_\\text{p}N_\\text{n}$ or $N_\\text{p}N_\\text{n}I$, where $N_\\text{p}$, $N_\\text{n}$, and $I$ are the number of valence protons (or holes), the number of valence neutrons (or holes), and the isospin of the parent nucleus, respectively. Fitting the $\\alpha$ preformation probabilities data extracted from the differences between experimental data and calculated half-lives without a shell correction, we give two analytic formulas of the $\\alpha$ preformation probabilities and the values of corresponding parameters. Using those formulas and the parameters, we calculate the $\\alp...

  8. Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing

    Science.gov (United States)

    Dilernia, Dario A.; Chien, Jung-Ting; Monaco, Daniela C.; Brown, Michael P.S.; Ende, Zachary; Deymier, Martin J.; Yue, Ling; Paxinos, Ellen E.; Allen, Susan; Tirado-Ramos, Alfredo; Hunter, Eric

    2015-01-01

    Single Molecule, Real-Time (SMRT®) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution. PMID:26101252

  9. Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing.

    Science.gov (United States)

    Dilernia, Dario A; Chien, Jung-Ting; Monaco, Daniela C; Brown, Michael P S; Ende, Zachary; Deymier, Martin J; Yue, Ling; Paxinos, Ellen E; Allen, Susan; Tirado-Ramos, Alfredo; Hunter, Eric

    2015-11-16

    Single Molecule, Real-Time (SMRT) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution.

  10. The absence of Arabidopsis-type telomeres in Cestrum and closely related genera Vestia and Sessea (Solanaceae): first evidence from eudicots.

    Science.gov (United States)

    Sykorova, Eva; Lim, Kar Yoong; Chase, Mark W; Knapp, Sandra; Leitch, Ilia Judith; Leitch, Andrew Rowland; Fajkus, Jiri

    2003-05-01

    Using slot-blot and fluorescent in situ hybridization (FISH), we found no evidence for the presence of the Arabidopsis-type telomeric sequence (TTTAGGG)n at the chromosome termini in any of the Cestrum species we investigated. Probing for the human-type telomere (TTAGGG)n also revealed no signal. However, polymerase chain reaction experiments indicated that there are short lengths of the sequence TTTAGGG dispersed in the genome but that these sequences are almost certainly too short to act as functional telomeres even if they were at the chromosome termini. An analysis of related genera Vestia and Sessea indicates that they too lack the Arabidopsis-type telomere, and the sequences were lost in the common ancestor of these genera. We found that the Cestrum species investigated had particularly large mean chromosome sizes. We discuss whether this is a consequence of alternative telomere end maintenance systems.

  11. Multiplicity of Galactic Cepheids from long-baseline interferometry - III. Sub-percent limits on the relative brightness of a close companion of δ Cephei

    Science.gov (United States)

    Gallenne, A.; Mérand, A.; Kervella, P.; Monnier, J. D.; Schaefer, G. H.; Roettenbacher, R. M.; Gieren, W.; Pietrzyński, G.; McAlister, H.; ten Brummelaar, T.; Sturmann, J.; Sturmann, L.; Turner, N.; Anderson, R. I.

    2016-09-01

    We report new CHARA/Michigan InfraRed Combiner interferometric observations of the Cepheid archetype δ Cep, which aimed at detecting the newly discovered spectroscopic companion. We reached a maximum dynamic range ΔH = 6.4, 5.8 and 5.2 mag, respectively, within the relative distance to the Cepheid r 9.15, 8.31 and 7.77 mag, respectively, for r < 25 mas, 25 < r < 50 mas and 50 < r < 100 mas. We also found that to be consistent with the predicted orbital period (Anderson et al.), the companion has to be located at a projected separation <24 mas with a spectral type later than an F0V star.

  12. Autonomic and eyeblink conditioning are closely related to contingency awareness: reply to Wiens and Ohman (2002) and Manns et al. (2002).

    Science.gov (United States)

    Shanks, David R; Lovibond, Peter F

    2002-01-01

    S. Wiens and A. Ohman (2002) disputed the conclusion that Pavlovian conditioning is strongly related to contingency awareness (P. F. Lovibond & D. R. Shanks, 2002) on the basis that an inappropriate definition of awareness was used. J. R. Manns, R. E. Clark, and L. R. Squire (2002) contended that delay eyeblink conditioning is independent of awareness. The authors of the present article consider these arguments, highlight several problems in the new studies described by the commentators, and conclude that there is still little evidence for unconscious conditioning in either subliminal autonomic conditioning or eyeblink conditioning. The most parsimonious account of existing data is that a single learning process gives rise to both awareness and conditioned responding. Further progress in evaluating the possibility of unconscious conditioning would be facilitated by the development of more completely specified and testable dual-process models.

  13. Sugar ratios, glutathione redox status and phenols in the resurrection species Haberlea rhodopensis and the closely related non-resurrection species Chirita eberhardtii.

    Science.gov (United States)

    Djilianov, D; Ivanov, S; Moyankova, D; Miteva, L; Kirova, E; Alexieva, V; Joudi, M; Peshev, D; Van den Ende, W

    2011-09-01

    Because of their unique tolerance to desiccation, the so-called resurrection plants can be considered as excellent models for extensive research on plant reactions to environmental stresses. The vegetative tissues of these species are able to withstand long dry periods and to recover very rapidly upon re-watering. This study follows the dynamics of key components involved in leaf tissue antioxidant systems under desiccation in the resurrection plant Haberlea rhodopensis and the related non-resurrection species Chirita eberhardtii. In H. rhodopensis these parameters were also followed during recovery after full drying. A well-defined test system was developed to characterise the different responses of the two species under drought stress. Results show that levels of H₂O₂ decreased significantly both in H. rhodopensis and C. eberhardtii, but that accumulation of malondialdehyde was much more pronounced in the desiccation-tolerant H. rhodopensis than in the non-resurrection C. eberhardtii. A putative protective role could be attributed to accumulation of total phenols in H. rhodopensis during the late stages of drying. The total glutathione concentration and GSSG/GSH ratio increased upon complete dehydration of H. rhodopensis. Our data on soluble sugars suggest that sugar ratios might be important for plant desiccation tolerance. An array of different adaptations could thus be responsible for the resurrection phenotype of H. rhodopensis.

  14. Correlations between major risk factors and closely related Mycobacterium tuberculosis isolates grouped by three current enotyping procedures: a population-based study in northeast Mexico

    Directory of Open Access Journals (Sweden)

    Katia Peñuelas-Urquides

    2014-09-01

    Full Text Available The characteristics of tuberculosis (TB patients related to a chain of recent TB transmissions were investigated. Mycobacterium tuberculosis (MTB isolates (120 were genotyped using the restriction fragment length polymorphism-IS6110 (R, spacer oligotyping (S and mycobacterial interspersed repetitive units-variable number of tandem repeats (M methods. The MTB isolates were clustered and the clusters were grouped according to the similarities of their genotypes. Spearman’s rank correlation coefficients between the groups of MTB isolates with similar genotypes and those patient characteristics indicating a risk for a pulmonary TB (PTB chain transmission were ana- lysed. The isolates showing similar genotypes were distributed as follows: SMR (5%, SM (12.5%, SR (1.67%, MR (0%, S (46.67%, M (5% and R (0%. The remaining 35 cases were orphans. SMR exhibited a significant correlation (p < 0.05 with visits to clinics, municipalities and comorbidities (primarily diabetes mellitus. S correlated with drug consumption and M with comorbidities. SMR is needed to identify a social network in metropolitan areas for PTB transmission and S and M are able to detect risk factors as secondary components of a transmission chain of TB.

  15. Correlations between major risk factors and closely related Mycobacterium tuberculosis isolates grouped by three current enotyping procedures: a population-based study in northeast Mexico

    Science.gov (United States)

    Peñuelas-Urquides, Katia; Martínez-Rodríguez, Herminia Guadalupe; Enciso-Moreno, José Antonio; Molina-Salinas, Gloria María; Silva-Ramírez, Beatriz; Padilla-Rivas, Gerardo Raymundo; Vera-Cabrera, Lucio; Torres-de-la-Cruz, Víctor Manuel; Martínez-Martínez, Yazmin Berenice; Ortega-García, Jorge Luis; Garza-Treviño, Elsa Nancy; Enciso-Moreno, Leonor; Saucedo-Cárdenas, Odila; Becerril-Montes, Pola; Said-Fernández/, Salvador

    2014-01-01

    The characteristics of tuberculosis (TB) patients related to a chain of recent TB transmissions were investigated. Mycobacterium tuberculosis (MTB) isolates (120) were genotyped using the restriction fragment length polymorphism-IS6110 (R), spacer oligotyping (S) and mycobacterial interspersed repetitive units-variable number of tandem repeats (M) methods. The MTB isolates were clustered and the clusters were grouped according to the similarities of their genotypes. Spearman’s rank correlation coefficients between the groups of MTB isolates with similar genotypes and those patient characteristics indicating a risk for a pulmonary TB (PTB) chain transmission were ana- lysed. The isolates showing similar genotypes were distributed as follows: SMR (5%), SM (12.5%), SR (1.67%), MR (0%), S (46.67%), M (5%) and R (0%). The remaining 35 cases were orphans. SMR exhibited a significant correlation (p < 0.05) with visits to clinics, municipalities and comorbidities (primarily diabetes mellitus). S correlated with drug consumption and M with comorbidities. SMR is needed to identify a social network in metropolitan areas for PTB transmission and S and M are able to detect risk factors as secondary components of a transmission chain of TB. PMID:25317710

  16. Correlations between major risk factors and closely related Mycobacterium tuberculosis isolates grouped by three current genotyping procedures: a population-based study in northeast Mexico.

    Science.gov (United States)

    Peñuelas-Urquides, Katia; Martínez-Rodríguez, Herminia Guadalupe; Enciso-Moreno, José Antonio; Molina-Salinas, Gloria María; Silva-Ramírez, Beatriz; Padilla-Rivas, Gerardo Raymundo; Vera-Cabrera, Lucio; Torres-de-la-Cruz, Víctor Manuel; Martínez-Martínez, Yazmin Berenice; Ortega-García, Jorge Luis; Garza-Treviño, Elsa Nancy; Enciso-Moreno, Leonor; Saucedo-Cárdenas, Odila; Becerril-Montes, Pola; Said-Fernández, Salvador

    2014-09-01

    The characteristics of tuberculosis (TB) patients related to a chain of recent TB transmissions were investigated. Mycobacterium tuberculosis (MTB) isolates (120) were genotyped using the restriction fragment length polymorphism-IS6110 (R), spacer oligotyping (S) and mycobacterial interspersed repetitive units-variable number of tandem repeats (M) methods. The MTB isolates were clustered and the clusters were grouped according to the similarities of their genotypes. Spearman's rank correlation coefficients between the groups of MTB isolates with similar genotypes and those patient characteristics indicating a risk for a pulmonary TB (PTB) chain transmission were ana- lysed. The isolates showing similar genotypes were distributed as follows: SMR (5%), SM (12.5%), SR (1.67%), MR (0%), S (46.67%), M (5%) and R (0%). The remaining 35 cases were orphans. SMR exhibited a significant correlation (p < 0.05) with visits to clinics, municipalities and comorbidities (primarily diabetes mellitus). S correlated with drug consumption and M with comorbidities. SMR is needed to identify a social network in metropolitan areas for PTB transmission and S and M are able to detect risk factors as secondary components of a transmission chain of TB.

  17. Transcription factor IID in the Archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes

    Science.gov (United States)

    Marsh, T. L.; Reich, C. I.; Whitelock, R. B.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1994-01-01

    The first step in transcription initiation in eukaryotes is mediated by the TATA-binding protein, a subunit of the transcription factor IID complex. We have cloned and sequenced the gene for a presumptive homolog of this eukaryotic protein from Thermococcus celer, a member of the Archaea (formerly archaebacteria). The protein encoded by the archaeal gene is a tandem repeat of a conserved domain, corresponding to the repeated domain in its eukaryotic counterparts. Molecular phylogenetic analyses of the two halves of the repeat are consistent with the duplication occurring before the divergence of the archael and eukaryotic domains. In conjunction with previous observations of similarity in RNA polymerase subunit composition and sequences and the finding of a transcription factor IIB-like sequence in Pyrococcus woesei (a relative of T. celer) it appears that major features of the eukaryotic transcription apparatus were well-established before the origin of eukaryotic cellular organization. The divergence between the two halves of the archael protein is less than that between the halves of the individual eukaryotic sequences, indicating that the average rate of sequence change in the archael protein has been less than in its eukaryotic counterparts. To the extent that this lower rate applies to the genome as a whole, a clearer picture of the early genes (and gene families) that gave rise to present-day genomes is more apt to emerge from the study of sequences from the Archaea than from the corresponding sequences from eukaryotes.

  18. Differential effects of liver steatosis on pharmacokinetic profile of two closely related hepatoselective NO-donors; V-PYRRO/NO and V-PROLI/NO.

    Science.gov (United States)

    Kus, Kamil; Kus, Edyta; Zakrzewska, Agnieszka; Jawien, Wojciech; Sitek, Barbara; Walczak, Maria; Chlopicki, Stefan

    2017-06-01

    To analyze the effect of liver steatosis and obesity on pharmacokinetic profile of two structurally-related liver-selective NO-donors - V-PYRRO/NO and V-PROLI/NO. C57BL/6 mice were fed control or high-fat diet for 15 weeks to induced liver steatosis and obesity (HFD mice). Pharmacokinetics and renal elimination studies were conducted in vivo following iv dosing of V-PYRRO/NO and V-PROLI/NO (0.03mmol/kg). Hepatic clearance was evaluated ex vivo in the isolated perfused mice liver and in vitro with the use of liver microsomes. V-PYRRO/NO and V-PROLI/NO, despite similar structure, displayed different pharmacokinetic properties. V-PYRRO/NO was uptaken and metabolized by the liver, while V-PROLI/NO was eliminated unchanged with urine. In HFD mice, despite increased CYP450 metabolism of V-PYRRO/NO the elimination rate was slower most likely due to the impairment of hepatic microcirculation caused by liver fat accumulation. In turn, in HFD mice renal clearence of V-PROLI/NO was accelerated and volume of distribution was increased most likely due to additional intracellular water in HFD mice. The pharmacokinetics of V-PROLI/NO, the novel proline-based analog of V-PYRRO/NO with additional single carboxylic acid moiety, attached to the molecule of V-PYRRO/NO to improve the water solubility, was differently affected by liver steatosis and obesity as compared with the parent compound V-PYRRO/NO. Copyright © 2017 Institute of Pharmacology, Polish Academy of Sciences. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

  19. Efficacy of potential phage cocktails against Vibrio harveyi and closely related Vibrio species isolated from shrimp aquaculture environment in the south east coast of India.

    Science.gov (United States)

    Stalin, Nattan; Srinivasan, Pappu

    2017-08-01

    A diverse set of novel phages infecting the marine pathogenic Vibrio harveyi was isolated from shrimp aquaculture environments in the south east coast of India. Based on initial screening, three phages with a broad host range revealed that the growth inhibition of phage is relatively specific to V. harveyi. They were also able to infect V. alginolyticus and V. parahemolyticus that belonged to the Harveyi clade species from shrimp pond and sea coast environment samples. However, the impact of these phages on their host bacterium are well understood; a one-step growth curve experiment and transmission electron microscope (TEM) revealed three phages grouped under the Myoviridae (VHM1 and VHM2); Siphoviridae (VHS1) family. These phages were further molecular characterized with respect to phage genomic DNA isolates. The randomly amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP) digestion with HindIII, and major structural proteins were distinguished by sodium-dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) clearly indicated that all the phage isolates were different, even when they came from the same source, giving an insight into the diversity of phages. Evaluation of microcosm studies of Penaeus monodon larvae infected with V. harveyi (105 CFU mL-1) showed that larvae survival after 96 h in the presence of phage treatment at 109 PFU mL-1 was enhanced when compared with the control. The resolution in over survival highly recommended that this study provides the phage-based therapy which could be an innovative and eco-friendly solution against Vibrio disease in shrimp aquaculture and in the natural environment. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Differential expression of interleukin-8 by polymorphonuclear leukocytes of two closely related species, Ovis canadensis and Ovis aries, in response to Mannheimia haemolytica infection.

    Science.gov (United States)

    Herndon, Caroline N; Foreyt, William J; Srikumaran, Subramaniam

    2010-08-01

    The pneumonic lesions and mortality caused by Mannheimia haemolytica in bighorn sheep (BHS; Ovis canadensis) are more severe than those in the related species, domestic sheep (DS; Ovis aries), under both natural and experimental conditions. Leukotoxin (Lkt) and lipopolysaccharide (LPS) are the most important virulence factors of this organism. One hallmark of pathogenesis of pneumonia is the influx of polymorphonuclear leukocytes (PMNs) into the lungs. Lkt-induced cytolysis of PMNs results in the release of cytotoxic compounds capable of damaging lung tissue. Interleukin-8 (IL-8) is a potent PMN chemoattractant. The objective of the present study was to determine if there is differential expression of IL-8 by the macrophages and PMNs of BHS and DS in response to M. haemolytica. Macrophages and PMNs of BHS and DS were stimulated with heat-killed M. haemolytica or LPS. IL-8 expression by the cells was measured by enzyme-linked immunosorbent assays and real-time reverse transcription-PCR (RT-PCR). The PMNs of BHS expressed severalfold higher levels of IL-8 than those of DS upon stimulation. Lesional lung tissue of M. haemolytica-infected BHS contained significantly higher levels of IL-8 than nonlesional tissue. The bronchoalveolar lavage (BAL) fluid of infected BHS also contained higher levels of IL-8 than that of infected DS. Depletion of IL-8 reduced migration of PMNs toward BAL fluid by approximately 50%, indicating that IL-8 is integral to PMN recruitment to the lung during M. haemolytica infection. Excessive production of IL-8, enhanced recruitment of PMNs, and PMN lysis by Lkt are likely responsible for the severity of the lung lesions in M. haemolytica-infected BHS.