Wood anatomy of the Euphorbiaceae, in particular of the subfamily Phyllanthoideae

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Mennega, Alberta M.W.

1985-01-01

The great variety in wood structure of the large family Euphorbiaceae makes it impossible to describe briefly a general wood pattern. Nevertheless, a more or less clear division into four anatomical groups can be made. A short overview is given of the wood structure of the uni-ovulate subfamilies

Systematics of the subfamily Poeciliinae Bonaparte (Cyprinodontiformes: Poeciliidae, with an emphasis on the tribe Cnesterodontini Hubbs

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Paulo Henrique Franco Lucinda

Full Text Available Osteological and soft anatomical features of representatives of poeciliine genera were studied to test the monophyly of the poeciliine tribes and to advance a hypothesis of relationships within the subfamily. The resultant hypothesis supports the proposal of a new classification for the subfamily Poeciliinae. Diagnoses are provided for suprageneric clades. The tribe Tomeurini is resurrected and the new tribes Brachyrhaphini and Priapichthyini as well as the supertribe Poeciliini are described. New usages of old tribe names are proposed based on the phylogenetic framework.

Phylogeny and evolutionary patterns in the Dwarf crayfish subfamily (Decapoda: Cambarellinae.

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Carlos Pedraza-Lara

Full Text Available The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group and into Central México (Mexican Group, has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We propose a comprehensive phylogenetic hypothesis for the subfamily based on mitochondrial and nuclear loci (3,833 bp using Bayesian and Maximum Likelihood methods. The phylogenetic structure found two phylogenetic groups associated to the two main geographic components (Gulf Group and Mexican Group and is partially consistent with the historical structure of river basins. The previous hypothesis, which divided the genus into three subgenera based on genitalia morphology was only partially supported (P = 0.047, resulting in a paraphyletic subgenus Pandicambarus. We found at least two cases in which phylogenetic structure failed to recover monophyly of recognized species while detecting several cases of cryptic diversity, corresponding to lineages not assigned to any described species. Cladogenetic patterns in the entire subfamily are better explained by an allopatric model of speciation. Diversification analyses showed similar cladogenesis patterns between both groups and did not significantly differ from the constant rate models. While cladogenesis in the Gulf Group is coincident in time with changes in the sea levels, in the Mexican Group, cladogenesis is congruent with the formation of the Trans-Mexican Volcanic Belt. Our results show how similar allopatric

Structure and dynamics of the human pleckstrin DEP domain: distinct molecular features of a novel DEP domain subfamily.

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Civera, Concepcion; Simon, Bernd; Stier, Gunter; Sattler, Michael; Macias, Maria J

2005-02-01

Pleckstrin1 is a major substrate for protein kinase C in platelets and leukocytes, and comprises a central DEP (disheveled, Egl-10, pleckstrin) domain, which is flanked by two PH (pleckstrin homology) domains. DEP domains display a unique alpha/beta fold and have been implicated in membrane binding utilizing different mechanisms. Using multiple sequence alignments and phylogenetic tree reconstructions, we find that 6 subfamilies of the DEP domain exist, of which pleckstrin represents a novel and distinct subfamily. To clarify structural determinants of the DEP fold and to gain further insight into the role of the DEP domain, we determined the three-dimensional structure of the pleckstrin DEP domain using heteronuclear NMR spectroscopy. Pleckstrin DEP shares main structural features with the DEP domains of disheveled and Epac, which belong to different DEP subfamilies. However, the pleckstrin DEP fold is distinct from these structures and contains an additional, short helix alpha4 inserted in the beta4-beta5 loop that exhibits increased backbone mobility as judged by NMR relaxation measurements. Based on sequence conservation, the helix alpha4 may also be present in the DEP domains of regulator of G-protein signaling (RGS) proteins, which are members of the same DEP subfamily. In pleckstrin, the DEP domain is surrounded by two PH domains. Structural analysis and charge complementarity suggest that the DEP domain may interact with the N-terminal PH domain in pleckstrin. Phosphorylation of the PH-DEP linker, which is required for pleckstrin function, could regulate such an intramolecular interaction. This suggests a role of the pleckstrin DEP domain in intramolecular domain interactions, which is distinct from the functions of other DEP domain subfamilies found so far.

Pollen morphology of the subfamily arecoideae griff. (family-arecaceae) from pakistan and kashmir

International Nuclear Information System (INIS)

Rasheed, A.A.; Perveen, A.; Abid, R.

2016-01-01

Pollen morphological characters are potentially informative in the systematic of monocotyledons including (Arecaceae), at supra and infra familial level. The pollen morphology of 8 species (subfamily Arecoideae) clearly shows that the qualitative pollen characters (such as aperture, exine pattern and shape) are found to be taxonomically important as compared to the quantitative characters (such as size of the grain and exine thickness).Considerable pollen variations have been found within the subfamily Arecoideae with regard to size, shape, aperture type and exine pattern. For instance, 7 out of 8 species have monosulcate pollen (i.e., 87.5%) and a remaining species (viz., Elaeis guineensis Jacq.) have trichotomosulcate pollen. The pollen are frequently elliptical, but in some cases rounded-triangular pollen were also found. Similarly, there is a great diversity in exine pattern such as punctate, reticulate, vermiculate, spinose, rugulate and perforate or combination of these types have also been found, but the most predominant pattern is the reticulate type. On the basis of pollen aperture, size and exine pattern, four pollen types have been recognized such as Areca-type, Dypsis-type, Cocos-type and Elaies-type. The data obtained from the palynological studies have been analyzed by Agglomerative cluster analysis choosing the Euclidean distance and Ward's method for a group linkage method. The objective of the present work is to classify studied taxa on the basis of pollen characters and to quantify the species relationships representing the subfamily Arecoideae based on numerical techniques. (author)

Unequal subfamily proportions among honey bee queen and worker brood

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Tilley; Oldroyd

1997-12-01

Queens from three colonies of feral honey bees, Apis mellifera were removed and placed in separate nucleus colonies. For each colony, eggs and larvae were taken from the nucleus and placed in the main hive on each of 3-4 consecutive weeks. Workers in the queenless parts selected young larvae to rear as queens. Queen pupae, together with the surrounding worker pupae, were removed from each colony and analysed at two to three microsatellite loci to determine their paternity. In all three colonies, the paternity of larvae chosen by the bees to rear as queens was not a random sample of the paternities in the worker brood, with certain subfamilies being over-represented in queens. These results support an important prediction of kin selection theory: when colonies are queenless, unequal relatedness within colonies could lead to the evolution of reproductive competition, that is some subfamilies achieving greater reproductive success than others. The mechanism by which such dominance is achieved could be through a system of kin recognition and nepotism, but we conclude that genetically based differential attractiveness of larvae for rearing as queens is more likely.Copyright 1997 The Association for the Study of Animal BehaviourCopyright 1997The Association for the Study of Animal Behaviour.

Variability of Pyrrolizidine Alkaloid Occurrence in Species of the Grass Subfamily Pooideae (Poaceae)

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Wesseling, Anne-Maria; Demetrowitsch, Tobias J.; Schwarz, Karin; Ober, Dietrich

2017-01-01

Pyrrolizidine alkaloids (PAs) are a class of secondary metabolites found in various unrelated angiosperm lineages including cool-season grasses (Poaceae, subfamily Pooideae). Thesinine conjugates, saturated forms of PA that are regarded as non-toxic, have been described to occur in the two grass species Lolium perenne and Festuca arundinacea (Poaceae, subfamily Pooideae). In a wider screen, we tested various species of the Pooideae lineage, grown under controlled conditions, for their ability to produce thesinine conjugates or related structures. Using an LC-MS based targeted metabolomics approach we were able to show that PA biosynthesis in grasses is limited to a group of very closely related Pooideae species that produce a limited diversity of PA structures. High variability in PA levels was observed even between individuals of the same species. These individual accumulation patterns are discussed with respect to a possible function and evolution of this type of alkaloid. PMID:29250094

Variability of Pyrrolizidine Alkaloid Occurrence in Species of the Grass Subfamily Pooideae (Poaceae

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Anne-Maria Wesseling

2017-11-01

Full Text Available Pyrrolizidine alkaloids (PAs are a class of secondary metabolites found in various unrelated angiosperm lineages including cool-season grasses (Poaceae, subfamily Pooideae. Thesinine conjugates, saturated forms of PA that are regarded as non-toxic, have been described to occur in the two grass species Lolium perenne and Festuca arundinacea (Poaceae, subfamily Pooideae. In a wider screen, we tested various species of the Pooideae lineage, grown under controlled conditions, for their ability to produce thesinine conjugates or related structures. Using an LC-MS based targeted metabolomics approach we were able to show that PA biosynthesis in grasses is limited to a group of very closely related Pooideae species that produce a limited diversity of PA structures. High variability in PA levels was observed even between individuals of the same species. These individual accumulation patterns are discussed with respect to a possible function and evolution of this type of alkaloid.

Gene Structures, Classification, and Expression Models of the DREB Transcription Factor Subfamily in Populus trichocarpa

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Yunlin Chen

2013-01-01

Full Text Available We identified 75 dehydration-responsive element-binding (DREB protein genes in Populus trichocarpa. We analyzed gene structures, phylogenies, domain duplications, genome localizations, and expression profiles. The phylogenic construction suggests that the PtrDREB gene subfamily can be classified broadly into six subtypes (DREB A-1 to A-6 in Populus. The chromosomal localizations of the PtrDREB genes indicated 18 segmental duplication events involving 36 genes and six redundant PtrDREB genes were involved in tandem duplication events. There were fewer introns in the PtrDREB subfamily. The motif composition of PtrDREB was highly conserved in the same subtype. We investigated expression profiles of this gene subfamily from different tissues and/or developmental stages. Sixteen genes present in the digital expression analysis had high levels of transcript accumulation. The microarray results suggest that 18 genes were upregulated. We further examined the stress responsiveness of 15 genes by qRT-PCR. A digital northern analysis showed that the PtrDREB17, 18, and 32 genes were highly induced in leaves under cold stress, and the same expression trends were shown by qRT-PCR. Taken together, these observations may lay the foundation for future functional analyses to unravel the biological roles of Populus’ DREB genes.

Identification of multiple distinct Snf2 subfamilies with conserved structural motifs.

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Flaus, Andrew; Martin, David M A; Barton, Geoffrey J; Owen-Hughes, Tom

2006-01-01

The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function.

HCV proteins and immunoglobulin variable gene (IgV) subfamilies in HCV-induced type II mixed cryoglobulinemia: a concurrent pathogenetic role.

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Sautto, Giuseppe; Mancini, Nicasio; Solforosi, Laura; Diotti, Roberta A; Clementi, Massimo; Burioni, Roberto

2012-01-01

The association between hepatitis C virus (HCV) infection and type II mixed cryoglobulinemia (MCII) is well established, but the role played by distinct HCV proteins and by specific components of the anti-HCV humoral immune response remains to be clearly defined. It is widely accepted that HCV drives the expansion of few B-cell clones expressing a restricted pool of selected immunoglobulin variable (IgV) gene subfamilies frequently endowed with rheumatoid factor (RF) activity. Moreover, the same IgV subfamilies are frequently observed in HCV-transformed malignant B-cell clones occasionally complicating MCII. In this paper, we analyze both the humoral and viral counterparts at the basis of cryoglobulins production in HCV-induced MCII, with particular attention reserved to the single IgV subfamilies most frequently involved.

Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates

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Yoder, Anne D.; Chan, Lauren M.; dos Reis, Mario; Larsen, Peter A.; Campbell, C. Ryan; Rasoloarison, Rodin; Barrett, Meredith; Roos, Christian; Kappeler, Peter; Bielawski, Joseph; Yang, Ziheng

2014-01-01

Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vomeronasal receptor class 1 (V1R) sequences ever generated for a diverse yet phylogenetically coherent group of mammals, the tooth-combed primates (suborder Strepsirrhini). Phylogenetic analysis confirms our intensive sampling from a single V1R subfamily, apparently unique to the strepsirrhine primates. We designate this subfamily as V1Rstrep. The subfamily retains extensive repertoires of gene copies that descend from an ancestral gene duplication that appears to have occurred prior to the diversification of all lemuriform primates excluding the basal genus Daubentonia (the aye-aye). We refer to the descendent clades as V1Rstrep-α and V1Rstrep-β. Comparison of the two clades reveals different amino acid compositions corresponding to the predicted ligand-binding site and thus potentially to altered functional profiles between the two. In agreement with previous studies of the mouse lemur (genus, Microcebus), the majority of V1Rstrep gene copies appear to be intact and under strong positive selection, particularly within transmembrane regions. Finally, despite the surprisingly high number of gene copies identified in this study, it is nonetheless probable that V1R diversity remains underestimated in these nonmodel primates and that complete characterization will be limited until high-coverage assembled genomes are available. PMID:24398377

Crystal structure of Staphylococcus aureus Zn-glyoxalase I: new subfamily of glyoxalase I family

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Chirgadze, Yuri N. [Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia; Boshkova, Eugenia A. [Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia; Battaile, Kevin P. [Advanced Photon Source, Argonne National Laboratory, Hauptman–Woodward Medical Research Institute, IMCA-CAT, Argonne, IL 60439, USA; Mendes, Vitor G. [Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; Lam, Robert [Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada; Chan, Tiffany S. Y. [Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada; Romanov, Vladimir [Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada; Pai, Emil F. [Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Chirgadze, Nickolay Y. [Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2C4, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada; X-CHIP Technologies Inc., Toronto, Ontario, Canada

2017-01-16

The crystal structures of protein SA0856 from Staphylococcus aureus in its apo-form and in complex with a Zn2+-ion have been presented. The 152 amino acid protein consists of two similar domains with α + β topology. In both crystalline state and in solution, the protein forms a dimer with monomers related by a twofold pseudo-symmetry rotation axis. A sequence homology search identified the protein as a member of the structural family Glyoxalase I. We have shown that the enzyme possesses glyoxalase I activity in the presence of Zn2+, Mg2+, Ni2+, and Co2+, in this order of preference. Sequence and structure comparisons revealed that human glyoxalase I should be assigned to a subfamily A, while S. aureus glyoxalase I represents a new subfamily B, which includes also proteins from other bacteria. Both subfamilies have a similar protein chain fold but rather diverse sequences. The active sites of human and staphylococcus glyoxalases I are also different: the former contains one Zn-ion per chain; the latter incorporates two of these ions. In the active site of SA0856, the first Zn-ion is well coordinated by His58, Glu60 from basic molecule and Glu40*, His44* from adjacent symmetry-related molecule. The second Zn3-ion is coordinated only by residue His143 from protein molecule and one acetate ion. We suggest that only single Zn1-ion plays the role of catalytic center. The newly found differences between the two subfamilies could guide the design of new drugs against S. aureus, an important pathogenic micro-organism.

HCV Proteins and Immunoglobulin Variable Gene (IgV Subfamilies in HCV-Induced Type II Mixed Cryoglobulinemia: A Concurrent Pathogenetic Role

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Giuseppe Sautto

2012-01-01

Full Text Available The association between hepatitis C virus (HCV infection and type II mixed cryoglobulinemia (MCII is well established, but the role played by distinct HCV proteins and by specific components of the anti-HCV humoral immune response remains to be clearly defined. It is widely accepted that HCV drives the expansion of few B-cell clones expressing a restricted pool of selected immunoglobulin variable (IgV gene subfamilies frequently endowed with rheumatoid factor (RF activity. Moreover, the same IgV subfamilies are frequently observed in HCV-transformed malignant B-cell clones occasionally complicating MCII. In this paper, we analyze both the humoral and viral counterparts at the basis of cryoglobulins production in HCV-induced MCII, with particular attention reserved to the single IgV subfamilies most frequently involved.

Flora of subfamily Prunoideae of family Rosaceae in botanical garden of Dnipropetrovsk university

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V. F. Opanasenko

2008-02-01

Full Text Available The present state of genofond of the 24 taxa collection of subfamily Prunoideae Focke (family Rosaceae Juss in DNU botanical garden has been analysed. Valuable genotypes for practical use in the development of landscape, farm horticulture and further selection were marked out. The ways of further exploit was planned.

Reassessment of Species Diversity of the Subfamily Denticollinae (Coleoptera: Elateridae through DNA Barcoding.

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Taeman Han

Full Text Available The subfamily Denticollinae is a taxonomically diverse group in the family Elateridae. Denticollinae includes many morphologically similar species and crop pests, as well as many undescribed species at each local fauna. To construct a rapid and reliable identification system for this subfamily, the effectiveness of molecular species identification was assessed based on 421 cytochrome c oxidase subunit I (COI sequences of 84 morphologically identified species. Among the 84 morphospecies, molecular species identification of 60 species (71.4% was consistent with their morphological identifications. Six cryptic and/or pseudocryptic species with large genetic divergence (>5% were confirmed by their sympatric or allopatric distributions. However, 18 species, including a subspecies, had ambiguous genetic distances and shared overlapping intra- and interspecific genetic distances (range: 2.12%-3.67% suggesting incomplete lineage sorting, introgression of mitochondrial genome, or affection by endosymbionts, such as Wolbachia infection, between species and simple genetic variation within species. In this study, we propose a conservative threshold of 3.6% for convenient molecular operational taxonomic unit (MOTU identification in the subfamily Denticollinae based on the results of pairwise genetic distances analyses using neighbor-joining, mothur, Automatic Barcode Gap Discovery analysis, and tree-based species delimitation by Poisson Tree Processes analysis. Using the 3.6% threshold, we identified 87 MOTUs and found 8 MOTUs in the interval between 2.5% to 3.5%. Evaluation of MOTUs identified in this range requires integrative species delimitation, including review of morphological and ecological differences as well as sensitive genetic markers. From this study, we confirmed that COI sequence is useful for reassessing species diversity for polymorphic and polytypic species occurring in sympatric and allopatric distributions, and for a single species having

Flight patterns and sex ratio of beetles of the subfamily Dynastinae (Coleoptera, Melolonthidae

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Larissa Simões Corrêa de Albuquerque

2016-09-01

Full Text Available ABSTRACT Dynastinae is one of the most representative subfamilies of Melolonthidae (Scarabaeoidea and has considerable ecological importance due mainly to interactions with plants of the families Araceae and Annonaceae. This relationship has led to the evolution of nocturnal activity patterns, which are influenced by environmental conditions. In the present study, abiotic factors were investigated to comprehend the influence on the flight patterns and identify the sex ratio of beetles from this subfamily. A study was conducted at Campo de Instrução Marechal Newton Cavalcanti in northeastern Brazil between December 2010 and November 2011. Thirteen species of Dynastinae were identified, most of which were from the genus Cyclocephala. Abundance and richness were greater in the dry season. Six species exhibited peak flight activity at specific periods of the night. More females than males were recorded for Cyclocephala distincta and C. paraguayensis. The present findings suggest that rainfall reduces the flight activity of these beetles and different time schedules may be related to mating behavior, foraging behavior and the avoidance of interspecific resource competition.

Revision of the subfamily Euphorinae (excluding the tribe Meteorini Cresson) (Hymenoptera: Braconidae) from China

NARCIS (Netherlands)

Chen, X.; Achterberg, van C.

1997-01-01

The subfamily Euphorinae (excluding the tribe Meteorini Cresson) (Hymenoptera: Braconidae) from China is revised. In total 150 species, belonging to 24 genera, are treated and keyed. One genus (Heia gen. nov.; type species: Heia robustipes spec. nov.) and 69 species are described as new to science.

Studies on Neotropical Phasmatodea XVI: Revision of Haplopodini Günther, 1953 (rev. stat.), with notes on the subfamily Cladomorphinae Bradley & Galil, 1977 and the descriptions of a new tribe, four new genera and nine new species (Phasmatodea: "Anareolatae": Phasmatidae: Cladomorphinae).

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Hennemann, Frank H; Conle, Oskar V; Perez-Gelabert, Daniel E

2016-06-27

eggs. Haplopodini Günther, 1953 is re-established (rev. stat.) and comprises almost exclusively Caribbean genera previously placed in Hesperophasmatini by Bradley & Galil (1977) or Cranidiini by Zompro, (2004). Aploploides Rehn & Hebard, 1938, Diapherodes Gray, 1835, Haplopus Burmeister, 1838 and Paracranidium Brock, 1998 were misplaced in Cranidiini and are transferred to Haplopodini. On the basis of numerous morphological characters of the insects and eggs Hesperophasmatini is removed from Pseudophasmatidae: Xerosomatinae and re-transferred to its previous position in the subfamily Cladomorphinae sensu lato. A detailed newdiagnosis of Hesperophasmatini is presented, but is only provisional since the true diversity is as yet only fractionally known. The lack of a gula distinguishes Hesperophasmatini from all other tribes. The genus Laciphorus Redtenbacher, 1908 is removed from Hesperophasmatini and transferred to Diapheromeridae: Diapheromerinae: Diapheromerini. The new tribe Pterinoxylini n. trib. is established to contain only the type-genus Pterinoxylus Audinet-Serville, 1838. It is closely related and perhaps the sister taxon of Hesperophasmatini, with which it shares the presence of rough sensory areas on the probasisternum and profurcasternum. It differs from Hesperophasmatini and Haplopodini by the presence of a tympanal region (= stridulatory organ) in the alae of females and the alveolar eggs, which possess peripheral opercular and polar structures. Haplopodini is likely to be the sister group of Pterinoxylini n. trib. + Hesperophasmatini.        The tribe Haplopodini rev. stat. is revised at the species level and comprises eight almost exclusively Caribbean genera, four of which are newly described. All eight genera now contained in Haplopodini are described in detail, differentiated from their closest relatives and their relationships and systematic position within Haplopodini are discussed. Keys and maps showing their distributions are presented

Characterization of ppGalNAc-T18, a member of the vertebrate-specific Y subfamily of UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferases.

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Li, Xing; Wang, Jing; Li, Wei; Xu, Yingjiao; Shao, Dong; Xie, Yinyin; Xie, Wenxian; Kubota, Tomomi; Narimatsu, Hisashi; Zhang, Yan

2012-05-01

The first step of mucin-type O-glycosylation is catalyzed by members of the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase (ppGalNAc-T; EC 2.4.1.41) family. Each member of this family has unique substrate specificity and expression profiles. In this report, we describe a new subfamily of ppGalNAc-Ts, designated the Y subfamily. The Y subfamily consists of four members, ppGalNAc-T8, -T9, -T17 and -T18, in which the conserved YDX(5)WGGENXE sequence in the Gal/GalNAc-T motif of ppGalNAc-Ts is mutated to LDX(5)YGGENXE. Phylogenetic analysis revealed that the Y subfamily members only exist in vertebrates. All four Y subfamily members lack in vitro GalNAc-transferase activity toward classical substrates possibly because of the UDP-GalNAc-binding pocket mutants. However, ppGalNAc-T18, the newly identified defining member, was localized in the endoplasmic reticulum rather than the Golgi apparatus in lung carcinoma cells. The knockdown of ppGalNAc-T18 altered cell morphology, proliferation potential and changed cell O-glycosylation. ppGalNAc-T18 can also modulate the in vitro GalNAc-transferase activity of ppGalNAc-T2 and -T10, suggesting that it may be a chaperone-like protein. These findings suggest that the new Y subfamily of ppGalNAc-Ts plays an important role in protein glycosylation; characterizing their functions will provide new insight into the role of ppGalNAc-Ts.

The phylogeny of the family Lacertidae (Reptilia) based on nuclear DNA sequences: convergent adaptations to arid habitats within the subfamily Eremiainae.

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Mayer, Werner; Pavlicev, Mihaela

2007-09-01

The family Lacertidae encompasses more than 250 species distributed in the Palearctis, Ethiopis and Orientalis. Lacertids have been subjected in the past to several morphological and molecular studies to establish their phylogeny. However, the problems of convergent adaptation in morphology and of excessively variable molecular markers have hampered the establishment of well supported deeper phylogenetic relationships. Particularly the adaptations to xeric environments have often been used to establish a scenario for the origin and radiation of major lineages within lacertids. Here we present a molecular phylogenetic study based on two nuclear marker genes and representatives of 37 lacertid genera and distinct species groups (as in the case of the collective genus Lacerta). Roughly 1600 bp of the nuclear rag1 and c-mos genes were sequenced and analyzed. While the results provide good support to the hitherto suggested main subfamilies of Gallotiinae (Gallotia and Psammodromus), Eremiainae and Lacertinae [Harris, D.J., Arnold, E.N., Thomas, R.H., 1998. Relationships of lacertid lizards (Reptilia: Lacertidae) estimated from mitochondrial DNA sequences and morphology. Proc. R. Soc. Lond. B 265, 1939-1948], they also suggest unexpected relationships. In particular, the oriental genus Takydromus, previously considered the sister-group to the three subfamilies, is nested within Lacertinae. Moreover, the genera within the Eremiainae are further divided into two groups, roughly corresponding to their respective geographical distributions in the Ethiopian and the Saharo-Eurasian ranges. The results support an independent origin of adaptations to xeric conditions in different subfamilies. The relationships within the subfamily Lacertinae could not be resolved with the markers used. The species groups of the collective genus Lacerta show a bush-like topology in the inferred Bayesian tree, suggesting rapid radiation. The composition of the subfamilies Eremiainae and Lacertinae

The tomato RLK superfamily: phylogeny and functional predictions about the role of the LRRII-RLK subfamily in antiviral defense.

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Sakamoto, Tetsu; Deguchi, Michihito; Brustolini, Otávio J B; Santos, Anésia A; Silva, Fabyano F; Fontes, Elizabeth P B

2012-12-02

Receptor-like kinases (RLKs) play key roles during development and in responses to the environment. Despite the relevance of the RLK family and the completion of the tomato genome sequencing, the tomato RLK family has not yet been characterized, and a framework for functional predictions of the members of the family is lacking. To generate a complete list of all the members of the tomato RLK family, we performed a phylogenetic analysis using the Arabidopsis family as a template. A total of 647 RLKs were identified in the tomato genome, which were organized into the same subfamily clades as Arabidopsis RLKs. Only eight of 58 RLK subfamilies exhibited specific expansion/reduction compared to their Arabidopsis counterparts. We also characterized the LRRII-RLK family by phylogeny, genomic analysis, expression profile and interaction with the virulence factor from begomoviruses, the nuclear shuttle protein (NSP). The LRRII subfamily members from tomato and Arabidopsis were highly conserved in both sequence and structure. Nevertheless, the majority of the orthologous pairs did not display similar conservation in the gene expression profile, indicating that these orthologs may have diverged in function after speciation. Based on the fact that members of the Arabidopsis LRRII subfamily (AtNIK1, AtNIK2 and AtNIK3) interact with the begomovirus nuclear shuttle protein (NSP), we examined whether the tomato orthologs of NIK, BAK1 and NsAK genes interact with NSP of Tomato Yellow Spot Virus (ToYSV). The tomato orthologs of NSP interactors, SlNIKs and SlNsAK, interacted specifically with NSP in yeast and displayed an expression pattern consistent with the pattern of geminivirus infection. In addition to suggesting a functional analogy between these phylogenetically classified orthologs, these results expand our previous observation that NSP-NIK interactions are neither virus-specific nor host-specific. The tomato RLK superfamily is made-up of 647 proteins that form a

The tomato RLK superfamily: phylogeny and functional predictions about the role of the LRRII-RLK subfamily in antiviral defense

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Sakamoto Tetsu

2012-12-01

Full Text Available Abstract Background Receptor-like kinases (RLKs play key roles during development and in responses to the environment. Despite the relevance of the RLK family and the completion of the tomato genome sequencing, the tomato RLK family has not yet been characterized, and a framework for functional predictions of the members of the family is lacking. Results To generate a complete list of all the members of the tomato RLK family, we performed a phylogenetic analysis using the Arabidopsis family as a template. A total of 647 RLKs were identified in the tomato genome, which were organized into the same subfamily clades as Arabidopsis RLKs. Only eight of 58 RLK subfamilies exhibited specific expansion/reduction compared to their Arabidopsis counterparts. We also characterized the LRRII-RLK family by phylogeny, genomic analysis, expression profile and interaction with the virulence factor from begomoviruses, the nuclear shuttle protein (NSP. The LRRII subfamily members from tomato and Arabidopsis were highly conserved in both sequence and structure. Nevertheless, the majority of the orthologous pairs did not display similar conservation in the gene expression profile, indicating that these orthologs may have diverged in function after speciation. Based on the fact that members of the Arabidopsis LRRII subfamily (AtNIK1, AtNIK2 and AtNIK3 interact with the begomovirus nuclear shuttle protein (NSP, we examined whether the tomato orthologs of NIK, BAK1 and NsAK genes interact with NSP of Tomato Yellow Spot Virus (ToYSV. The tomato orthologs of NSP interactors, SlNIKs and SlNsAK, interacted specifically with NSP in yeast and displayed an expression pattern consistent with the pattern of geminivirus infection. In addition to suggesting a functional analogy between these phylogenetically classified orthologs, these results expand our previous observation that NSP-NIK interactions are neither virus-specific nor host-specific. Conclusions The tomato RLK

Current status of subfamily Ichneumoninae (Hymenoptera: Ichneumonidae) from Malaysia and Singapore

Science.gov (United States)

Norhafiza, A. F.; Idris, A. B.

2013-11-01

In this paper, 25 genera and 38 species under 10 tribes (Alomyini, Compsophorini, Goedartiini, Heresiarchini, Ichneumonini, Ischnojoppini, Joppocryptini, Listrodromini, Oedicephalini and Platylabini) of the subfamily Ichneumoninae housed in the Centre for Insect Systematics, UKM and Raffles Museum of Biodiversity Research (National University of Singapore) are reported from Malaysia and Singapore. The tribe Heresiarchini has the greatest number of species (13) followed by Ichneumonini with six species. Imeria is the largest genus which contains five species recorded. Six species in this study are new records for Malaysia.

First contact pheromone identified for a longhorned beetle (Coleoptera: Cerambycidae) in the subfamily Prioninae

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Annie E. Spikes; Matthew A. Paschen; Jocelyn G. Miller; Jardel A. Moreira; Paul B. Hamel; Nathan M. Schiff; Matthew D. Ginzel

2010-01-01

Little is known of the reproductive behavior of longhorned beetles (Coleoptera: Cerambycidae) in the subfamily Prioninae. Mallodon dasystomus (Say), the hardwood stump borer, is a widely distributed prionine that is native to the southern U.S. Here, we explored the chemically-mediated mating behavior of M dasystomus, and tested the hypothesis that males recognize...

Origin and evolution of GALA-LRR, a new member of the CC-LRR subfamily: from plants to bacteria?

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Andrey V Kajava

Full Text Available The phytopathogenic bacterium Ralstonia solanacearum encodes type III effectors, called GALA proteins, which contain F-box and LRR domains. The GALA LRRs do not perfectly fit any of the previously described LRR subfamilies. By applying protein sequence analysis and structural prediction, we clarify this ambiguous case of LRR classification and assign GALA-LRRs to CC-LRR subfamily. We demonstrate that side-by-side packing of LRRs in the 3D structures may control the limits of repeat variability within the LRR subfamilies during evolution. The LRR packing can be used as a criterion, complementing the repeat sequences, to classify newly identified LRR domains. Our phylogenetic analysis of F-box domains proposes the lateral gene transfer of bacterial GALA proteins from host plants. We also present an evolutionary scenario which can explain the transformation of the original plant LRRs into slightly different bacterial LRRs. The examination of the selective evolutionary pressure acting on GALA proteins suggests that the convex side of their horse-shoe shaped LRR domains is more prone to positive selection than the concave side, and we therefore hypothesize that the convex surface might be the site of protein binding relevant to the adaptor function of the F-box GALA proteins. This conclusion provides a strong background for further functional studies aimed at determining the role of these type III effectors in the virulence of R. solanacearum.

Identification and characterization of a novel gene differentially expressed in zebrafish cross-subfamily cloned embryos

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Wang Ya-Ping

2008-03-01

Full Text Available Abstract Background Cross-species nuclear transfer has been shown to be a potent approach to retain the genetic viability of a certain species near extinction. However, most embryos produced by cross-species nuclear transfer were compromised because that they were unable to develop to later stages. Gene expression analysis of cross-species cloned embryos will yield new insights into the regulatory mechanisms involved in cross-species nuclear transfer and embryonic development. Results A novel gene, K31, was identified as an up-regulated gene in fish cross-subfamily cloned embryos using SSH approach and RACE method. K31 complete cDNA sequence is 1106 base pairs (bp in length, with a 342 bp open reading frame (ORF encoding a putative protein of 113 amino acids (aa. Comparative analysis revealed no homologous known gene in zebrafish and other species database. K31 protein contains a putative transmembrane helix and five putative phosphorylation sites but without a signal peptide. Expression pattern analysis by real time RT-PCR and whole-mount in situ hybridization (WISH shows that it has the characteristics of constitutively expressed gene. Sub-cellular localization assay shows that K31 protein can not penetrate the nuclei. Interestingly, over-expression of K31 gene can cause lethality in the epithelioma papulosum cyprinid (EPC cells in cell culture, which gave hint to the inefficient reprogramming events occurred in cloned embryos. Conclusion Taken together, our findings indicated that K31 gene is a novel gene differentially expressed in fish cross-subfamily cloned embryos and over-expression of K31 gene can cause lethality of cultured fish cells. To our knowledge, this is the first report on the determination of novel genes involved in nucleo-cytoplasmic interaction of fish cross-subfamily cloned embryos.

RINL, guanine nucleotide exchange factor Rab5-subfamily, is involved in the EphA8-degradation pathway with odin.

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Hiroaki Kajiho

Full Text Available The Rab family of small guanosine triphosphatases (GTPases plays a vital role in membrane trafficking. Its active GTP-bound state is driven by guanine nucleotide-exchange factors (GEFs. Ras and Rab interactor (or Ras interaction/interference-like (RINL, which contains a conserved VPS9 domain critical for GEF action, was recently identified as a new Rab5 subfamily GEF in vitro. However, its detailed function and interacting molecules have not yet been fully elucidated. Here we found that RINL has GEF activity for the Rab5 subfamily proteins by measuring their GTP-bound forms in cultured cells. We also found that RINL interacts with odin, a member of the ankyrin-repeat and sterile-alpha motif (SAM domain-containing (Anks protein family. In addition, the Eph tyrosine kinase receptor EphA8 formed a ternary complex with both RINL and odin. Interestingly, RINL expression in cultured cells reduced EphA8 levels in a manner dependent on both its GEF activity and interaction with odin. In addition, knockdown of RINL increased EphA8 level in HeLa cells. Our findings suggest that RINL, as a GEF for Rab5 subfamily, is implicated in the EphA8-degradation pathway via its interaction with odin.

Functional interactome of Aquaporin 1 sub-family reveals new physiological functions in Arabidopsis Thaliana

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Mohamed Ragab Abdel Gawwad

2013-09-01

Full Text Available Aquaporins are channel proteins found in plasma membranes and intercellular membranes of different cellular compartments, facilitate the water flux, solutes and gases across the cellular plasma membranes. The present study highlights the sub-family plasma membrane intrinsic protein (PIP predicting the 3-D structure and analyzing the functional interactome of it homologs. PIP1 homologs integrate with many proteins with different plant physiological roles in Arabidopsis thaliana including; PIP1A and PIP1B: facilitate the transport of water, diffusion of amino acids and/or peptides from the vacuolar compartment to the cytoplasm, play a role in the control of cell turgor and cell expansion and involved in root water uptake respectively. In addition we found that PIP1B plays a defensive role against Pseudomonas syringae infection through the interaction with the plasma membrane Rps2 protein. Another substantial function of PIP1C via the interaction with PIP2E is the response to nematode infection. Generally, PIP1 sub-family interactome controlling many physiological processes in plant cell like; osmoregulation in plants under high osmotic stress such as under a high salt, response to nematode, facilitate the transport of water across cell membrane and regulation of floral initiation in Arabidopsis thaliana.

Checklist of the subfamilies Mirinae and Orthotylinae (Hemiptera: Heteroptera: Miridae in western parts of Kerman Province, Iran

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Mohsen Shamsi

2014-03-01

Full Text Available A faunal study was carried out on the subfamilies Mirinae and Orthotylinae (Heteroptera: Miridae from different parts of western Kerman Province on various host plants. In total 16 species belonging to 14 genera were collected and identified from different host plants and localities.

ROLE OF ATP BINDING CASSETTE SUB-FAMILY MEMBER 2 (ABCG2) IN MOUSE EMBRYONIC STEM CELL DEVELOPMENT.

Science.gov (United States)

ATP binding cassette sub-family member 2 (ABCG2), is a member of the ABC transporter superfamily and a principal xenobiotic transporter. ABCG2 is also highly expressed in certain stem cell populations where it is thought to be related to stem cell plasticity, although the role o...

Frames of exponentials:lower frame bounds for finite subfamilies, and approximation of the inverse frame operator

DEFF Research Database (Denmark)

Christensen, Ole; Lindner, Alexander M

2001-01-01

We give lower frame bounds for finite subfamilies of a frame of exponentials {e(i lambdak(.))}k is an element ofZ in L-2(-pi,pi). We also present a method for approximation of the inverse frame operator corresponding to {e(i lambdak(.))}k is an element ofZ, where knowledge of the frame bounds for...

Australian water mites of the subfamily Notoaturinae Besch (Acari: Hydrachnidia: Aturidae), with the description of 24 new species

NARCIS (Netherlands)

Smit, H.

2010-01-01

New data are presented on the subfamily Notoaturinae from Australia. Twenty-four new species are described: Austraturus aculeatus n. sp., A. canaliculatus n. sp., A. lamingtonensis n. sp., A. longigenitalis n. sp., A. montanus n. sp., A. otwayensis n. sp., A. tasmanicus n. sp., Azugaturus

Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts.

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Asakura, Yukari; Bayraktar, Omer Ali; Barkan, Alice

2008-11-01

Chloroplast genomes in angiosperms encode approximately 20 group II introns, approximately half of which are classified as subgroup IIB. The splicing of all but one of the subgroup IIB introns requires a heterodimer containing the peptidyl-tRNA hydrolase homolog CRS2 and one of two closely related proteins, CAF1 or CAF2, that harbor a recently recognized RNA binding domain called the CRM domain. Two CRS2/CAF-dependent introns require, in addition, a CRM domain protein called CFM2 that is only distantly related to CAF1 and CAF2. Here, we show that CFM3, a close relative of CFM2, associates in vivo with those CRS2/CAF-dependent introns that are not CFM2 ligands. Mutant phenotypes in rice and Arabidopsis support a role for CFM3 in the splicing of most of the introns with which it associates. These results show that either CAF1 or CAF2 and either CFM2 or CFM3 simultaneously bind most chloroplast subgroup IIB introns in vivo, and that the CAF and CFM subunits play nonredundant roles in splicing. These results suggest that the expansion of the CRM protein family in plants resulted in two subfamilies that play different roles in group II intron splicing, with further diversification within a subfamily to accommodate multiple intron ligands.

Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR.

Science.gov (United States)

Oueslati, Amel; Ollitrault, Frederique; Baraket, Ghada; Salhi-Hannachi, Amel; Navarro, Luis; Ollitrault, Patrick

2016-08-18

Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations. The objective of our work was to demonstrate that a molecular taxonomic key based on easy, scalable and low-cost genotyping method should be developed from a set of Single Nucleotide Polymorphisms (SNPs) diagnostic of well-established clades. It was applied to the Aurantioideae subfamily, the largest group of the Rutaceae family that includes the cultivated citrus species. The publicly available nucleotide sequences of eight plastid genomic regions were compared for 79 accessions of the Aurantioideae subfamily to search for SNPs revealing taxonomic differentiation at the inter-tribe, inter-subtribe, inter-genus and interspecific levels. Diagnostic SNPs (DSNPs) were found for 46 of the 54 clade levels analysed. Forty DSNPs were selected to develop KASPar markers and their taxonomic value was tested by genotyping 108 accessions of the Aurantioideae subfamily. Twenty-seven markers diagnostic of 24 clades were validated and they displayed a very high rate of transferability in the Aurantioideae subfamily (only 1.2 % of missing data on average). The UPGMA from the validated markers produced a cladistic organisation that was highly coherent with the previous phylogenetic analysis based on the sequence data of the eight plasmid regions. In particular, the monophyletic origin of the "true citrus" genera plus Oxanthera was validated. However, some clarification remains necessary regarding the organisation of the other wild species of the Citreae tribe. We validated the concept that with well-established clades, DSNPs can be selected and efficiently transformed into competitive allele-specific PCR markers (KASPar method) allowing cost-effective highly efficient cladistic analysis in large collections at

Comparative Mitogenomic Analysis of Species Representing Six Subfamilies in the Family Tenebrionidae

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Hong-Li Zhang

2016-05-01

Full Text Available To better understand the architecture and evolution of the mitochondrial genome (mitogenome, mitogenomes of ten specimens representing six subfamilies in Tenebrionidae were selected, and comparative analysis of these mitogenomes was carried out in this study. Ten mitogenomes in this family share a similar gene composition, gene order, nucleotide composition, and codon usage. In addition, our results show that nucleotide bias was strongly influenced by the preference of codon usage for A/T rich codons which significantly correlated with the G + C content of protein coding genes (PCGs. Evolutionary rate analyses reveal that all PCGs have been subjected to a purifying selection, whereas 13 PCGs displayed different evolution rates, among which ATPase subunit 8 (ATP8 showed the highest evolutionary rate. We inferred the secondary structure for all RNA genes of Tenebrio molitor (Te2 and used this as the basis for comparison with the same genes from other Tenebrionidae mitogenomes. Some conserved helices (stems and loops of RNA structures were found in different domains of ribosomal RNAs (rRNAs and the cloverleaf structure of transfer RNAs (tRNAs. With regard to the AT-rich region, we analyzed tandem repeat sequences located in this region and identified some essential elements including T stretches, the consensus motif at the flanking regions of T stretch, and the secondary structure formed by the motif at the 3′ end of T stretch in major strand, which are highly conserved in these species. Furthermore, phylogenetic analyses using mitogenomic data strongly support the relationships among six subfamilies: ((Tenebrionidae incertae sedis + (Diaperinae + Tenebrioninae + (Pimeliinae + Lagriinae, which is consistent with phylogenetic results based on morphological traits.

Role for ribosome-associated complex and stress-seventy subfamily B (RAC-Ssb) in integral membrane protein translation.

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Acosta-Sampson, Ligia; Döring, Kristina; Lin, Yuping; Yu, Vivian Y; Bukau, Bernd; Kramer, Günter; Cate, Jamie H D

2017-12-01

Targeting of most integral membrane proteins to the endoplasmic reticulum is controlled by the signal recognition particle, which recognizes a hydrophobic signal sequence near the protein N terminus. Proper folding of these proteins is monitored by the unfolded protein response and involves protein degradation pathways to ensure quality control. Here, we identify a new pathway for quality control of major facilitator superfamily transporters that occurs before the first transmembrane helix, the signal sequence recognized by the signal recognition particle, is made by the ribosome. Increased rates of translation elongation of the N-terminal sequence of these integral membrane proteins can divert the nascent protein chains to the ribosome-associated complex and stress-seventy subfamily B chaperones. We also show that quality control of integral membrane proteins by ribosome-associated complex-stress-seventy subfamily B couples translation rate to the unfolded protein response, which has implications for understanding mechanisms underlying human disease and protein production in biotechnology. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Rediscovered and new perisphaerine cockroaches from SW China with a review of subfamilial diagnosis (Blattodea: Blaberidae).

Science.gov (United States)

Li, Xin-Ran; Wang, Li-Li; Wang, Zong-Qing

2018-04-17

The taxonomic records of Chinese perisphaerine cockroaches were scattered in literature, and therefore a dedicated study is desired to update our knowledge. This paper reviews the subfamilial diagnosis and Chinese species, mostly from southwestern China. We provide high-definition habitus photos and drawings, the latter emphasizes the genitalia of both sexes, which are generalized with diagrams, abstracted from specimens examined. A total of 18 species are recorded in four genera, including Perisphaerus, or pill cockroach, the type genus of the subfamily. Two new genera and three new species are proposed: Achatiblatta achates gen. sp. nov., Frumentiforma frumentiformis gen. sp. nov., and Pseudoglomeris montana sp. nov.. Pseudoglomeris has five new junior synonyms: Corydidarum, Trichoblatta, Kurokia, Glomerexis, and Glomeriblatta; the following combinations are thus revived or new: Ps. aerea comb. nov., Ps. angustifolia comb. nov., Ps. beybienkoi comb. nov., Ps. fallax comb. nov., Ps. magnifica comb. rev., Ps. montshadskii comb. nov., Ps. nigra comb. nov., Ps. sculpta comb. nov., Ps. semisulcata comb. rev., Ps. tibetana comb. nov., and Ps. valida moderata comb. nov.. The following species are revalidated and combinations revived: Pe. pygmaeus comb. rev., Ps. dubia comb. sp. rev., and Ps. planiuscla comb. sp. rev.

Molecular Evolution of the CYP2D Subfamily in Primates: Purifying Selection on Substrate Recognition Sites without the Frequent or Long-Tract Gene Conversion

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Yasukochi, Yoshiki; Satta, Yoko

2015-01-01

The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences. PMID:25808902

A consistent nomenclature of antimicrobial peptides isolated from frogs of the subfamily Phyllomedusinae.

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Amiche, Mohamed; Ladram, Ali; Nicolas, Pierre

2008-11-01

A growing number of cationic antimicrobial peptides have been isolated from the skin of hylid frogs belonging to the Phyllomedusinae subfamily. The amino acid sequences of these peptides are currently located in several databases under identifiers with no consistent system of nomenclature to describe them. In order to provide a workable terminology for antimicrobial peptides from Phyllomedusid frogs, we have made a systematic effort to collect, analyze, and classify all the Phyllomedusid peptide sequences available in databases. We propose that frogs belonging to the Phyllomedusinae subfamily should be described by the species names set out in Amphibian Species of the World: http://research.amnh.org/herpetology/amphibia/index.php, American Museum of Natural History, New York, USA. Multiple alignments analysis of at least 80 antimicrobial peptides isolated from 12 Phyllomedusinae species were distributed in seven distinct peptide families including dermaseptin, phylloseptin, plasticin, dermatoxin, phylloxin, hyposin and orphan peptides, and will be considered as the name of the headgroup of each family. The parent peptide's name should be followed by the first upper letter of the species for orthologous peptides and publication date determines priority. For example, the abbreviation B for bicolor and H for hypochondrialis. When two species begin with the same letter, two letters in upper case should be used (the first letter followed by the second or the third letter and so on). For example, the abbreviation DI for distincta, DU for duellmani, VA for vaillanti and VN for vanzolinii. Paralogous peptides should bear letter(s) in upper case followed by numbers.

Whole genome identification, phylogeny and evolution of the cytochrome P450 family 2 (CYP2) sub-families in birds

DEFF Research Database (Denmark)

Almeida, Daniela; Maldonado, Emanuel; Khan, Imran

2016-01-01

The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 novel avian who...

The first mitochondrial genome for the fishfly subfamily Chauliodinae and implications for the higher phylogeny of Megaloptera.

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Yuyu Wang

Full Text Available Megaloptera are a basal holometabolous insect order with larvae exclusively predacious and aquatic. The evolutionary history of Megaloptera attracts great interest because of its antiquity and important systematic status in Holometabola. However, due to the difficulties identifying morphological apomorphies for the group, controversial hypotheses on the monophyly and higher phylogeny of Megaloptera have been proposed. Herein, we describe the complete mitochondrial (mt genome of a fishfly species, Neochauliodes punctatolosus Liu & Yang, 2006, representing the first mt genome of the subfamily Chauliodinae. A phylogenomic analysis was carried out based on the mt genomic sequences of 13 mt protein-coding genes (PCGs and two rRNA genes of nine Neuropterida species, comprising all three orders of Neuropterida and all families and subfamilies of Megaloptera. Both maximum likelihood and Bayesian inference analyses highly support the monophyly of Megaloptera, which was recovered as the sister of Neuroptera. Within Megaloptera, the sister relationship between Corydalinae and Chauliodinae was corroborated. The divergence time estimation suggests that stem lineage of Neuropterida and Coleoptera separated in the Early Permian. The interordinal divergence within Neuropterida might have occurred in the Late Permian.

Molecular Phylogenetics of the Serranid Subfamily Epinephelinae: Speciation and Biogeography in a Nearshore Marine Fish Clade

OpenAIRE

Craig, Matthew T,

2005-01-01

The processes that shape present day distributions of marine organisms have remained a central topic in evolutionary biology, conservation biology, and ecology. In this thesis, genetic data from mitochondrial and nuclear genes were used to create a phylogenetic hypothesis for the groupers of the subfamily Epinephelinae as a means of evaluating the current taxonomy of the group and the geography of speciation in marine organisms. The molecular phylogenetic hypothesis presented in Chap...

Molecular cloning and 3D model of first cytochrome P450 from CYP3A subfamily in saltwater crocodile (Crocodylus porosus).

Science.gov (United States)

Tabassum, Rabia

2017-10-18

Cytochrome P450s (CYPs) play critical role in oxidative metabolism of numerous xenobiotics and endogenous compounds. The first CYP3A subfamily member in saltwater crocodile has been cloned and modelled for three-dimensional (3D) structure. The full-length cDNA was obtained employing reverse transcription polymerase chain reaction (RT-PCR) strategy and rapid amplification of cDNA ends (RACE). The cDNA sequence of 1659 nucleotides includes 132 nucleotides from 5' untranslated region (UTR), an open reading frame of 1527 nucleotides encoding 509 amino acids designated as CYP3A163. The alignment of CYP3A163 sequence with CYP3A subfamily across the lineages exhibit the loss of 1 residue in birds and 7 residues in mammals in comparison to reptiles suggesting the adaptation processes during evolution. The amino acid identity of CYP3A163 with Alligator mississippiensis CYP3A77 and Homo sapiens CYP3A4 is 91% and 62% respectively. The 3D structure of CYP3A163 modelled using human CYP3A4 structure as a template with Phyre 2 software, represents high similarity with its functionally important motifs and catalytic domain. Both sequence and structure of CYP3A163 display the common and conserved features of CYP3A subfamily. Overall, this study provides primary molecular and structural data of CYP3A163 required to investigate the xenobiotic metabolism in saltwater crocodiles. Copyright © 2017 Elsevier Inc. All rights reserved.

Alu Sb2 subfamily is present in all higher primates but was most succesfully amplified in humans

Energy Technology Data Exchange (ETDEWEB)

Richer, C.; Zietkiewicz, E.; Labuda, D. [Universite de Montreal, Que (Canada)

1994-09-01

Alu repeats can be classified into subfamilies which amplified in primate genomes at different evolutionary time periods. A young Alu subfamily, Sb2, with a characteristic 7-nucleotide duplication at position 256, has been described in seven human loci. An Sb2 insertion found near the HD gene was unique to two HD families, indicating that Sb2 was still retropositionally active. Here, we have shown that the Sb2 insertion in the CHOL locus was similarly rare, being absent in 120 individuals of Caucasian, Oriental and Black origin. In contrast, Sb2 inserts in five other loci were found fixed (non-polymorphic), based on measurements in the same population sample, but absent from orthologous positions in higher apes. This suggest that Sb2 repeats spread relatively early in the human lineage following divergence from other primates and that these elements may be human-specific. By quantitative PCR, we investigated the presence of Sb2 sequences in different primate DNA, using one PCR primer anchored at the 5{prime} Alu-end and the other complementary to the duplicated Sb2-specific segment. With an Sb2-containing plasmid as a standard, we estimated the number of Sb2 repeats at 1500-1800 copies per human haploid equivalent; corresponding numbers in chimpanzee and gorilla were almost two orders of magnitude lower, while the signal observed in orangutan and gibbon DNAs was consistent with the presence of a single copy. The analysis of 22 human, 11 chimpanzee and 10 gorilla sequences indicates that the Alu Sb2 dispersed independently in these three primate lineages; gorilla consensus differs from the human Sb2 sequence by one position, while all chimpanzee repeats have their linker expanded by up to eight A-residues. Should they be thus considered as separate subfamilies? It is possible that sequence modifications with respect to the human consensus are responsible for poor retroposition of Sb2 in apes.

Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies.

Science.gov (United States)

Fetterman, Christina D; Rannala, Bruce; Walter, Michael A

2008-09-24

Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and

Current knowledge on bioacoustics of the subfamily Lophyohylinae (Hylidae, Anura and description of Ocellated treefrog Itapotihyla langsdorffii vocalizations

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Lucas Rodriguez Forti

2018-05-01

Full Text Available Background Anuran vocalizations, such as advertisement and release calls, are informative for taxonomy because species recognition can be based on those signals. Thus, a proper acoustic description of the calls may support taxonomic decisions and may contribute to knowledge about amphibian phylogeny. Methods Here we present a perspective on advertisement call descriptions of the frog subfamily Lophyohylinae, through a literature review and a spatial analysis presenting bioacoustic coldspots (sites with high diversity of species lacking advertisement call descriptions for this taxonomic group. Additionally, we describe the advertisement and release calls of the still poorly known treefrog, Itapotihyla langsdorffii. We analyzed recordings of six males using the software Raven Pro 1.4 and calculated the coefficient of variation for classifying static and dynamic acoustic properties. Results and Discussion We found that more than half of the species within the subfamily do not have their vocalizations described yet. Most of these species are distributed in the western and northern Amazon, where recording sampling effort should be strengthened in order to fill these gaps. The advertisement call of I. langsdorffii is composed of 3–18 short unpulsed notes (mean of 13 ms long, presents harmonic structure, and has a peak dominant frequency of about 1.4 kHz. This call usually presents amplitude modulation, with decreasing intensity along the sequence of notes. The release call is a simple unpulsed note with an average duration of 9 ms, and peak dominant frequency around 1.8 kHz. Temporal properties presented higher variations than spectral properties at both intra- and inter-individual levels. However, only peak dominant frequency was static at intra-individual level. High variability in temporal properties and lower variations related to spectral ones is usual for anurans; The first set of variables is determined by social environment or temperature

Taxonomy of the genus Brachyteles Spix, 1823 and its phylogenetic position within the subfamily Atelinae Gray, 1825

OpenAIRE

José Eduardo Serrano Villavicencio

2016-01-01

Muriquis, genus Brachyteles Spix, 1823, are the largest of the extant New World primates, and they are one of the three extant genera of the subfamily Atelinae along with Ateles (spider monkeys) and Lagothrix (wooly monkeys). The taxonomy of Brachyteles has constantly changed since its first description in the 19th century. First treated as a monotypic genus, and after several modifications in the number of species, Brachyteles currently contains two species, B. arachnoides (Southern muriqui)...

Subcellular location of Arabidopsis thaliana subfamily a1 β-galactosidases and developmental regulation of transcript levels of their coding genes.

Science.gov (United States)

Moneo-Sánchez, María; Izquierdo, Lucía; Martín, Ignacio; Labrador, Emilia; Dopico, Berta

2016-12-01

The aim of this work is to gain insight into the six members of the a1 subfamily of the β-galactosidases (BGAL) from Arabidopsis thaliana. First, the subcellular location of all these six BGAL proteins from a1 subfamily has been established in the cell wall by the construction of transgenic plants producing the enhanced green fluorescent protein (eGFP) fused to the BGAL proteins. BGAL12 is also located in the endoplasmic reticulum. Our study of the AtBGAL transcript accumulation along plant development indicated that all AtBGAL transcript appeared in initial stages of development, both dark- and light-grown seedlings, being AtBGAL1, AtBGAL2 and AtBGAL3 transcripts the predominant ones in the latter condition, mainly in the aerial part and with levels decreasing with age. The high accumulation of transcript of AtBGAL4 in basal internodes and in leaves at the end of development, and their strong increase after treatment both with BL and H 3 BO 3 point to an involvement of BGAL4 in cell wall changes leading to the cease of elongation and increased rigidity. The changes of AtBGAL transcript accumulation in relation to different stages and conditions of plant development, suggest that each of the different gene products have a plant-specific function and provides support for the proposed function of the subfamily a1 BGAL in plant cell wall remodelling for cell expansion or for cell response to stress conditions. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies

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Rannala Bruce

2008-09-01

Full Text Available Abstract Background Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Results Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Conclusion Consideration of selection pressures observed in conjunction with known

A Rationally Designed Agonist Defines Subfamily IIIA Abscisic Acid Receptors As Critical Targets for Manipulating Transpiration.

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Vaidya, Aditya S; Peterson, Francis C; Yarmolinsky, Dmitry; Merilo, Ebe; Verstraeten, Inge; Park, Sang-Youl; Elzinga, Dezi; Kaundal, Amita; Helander, Jonathan; Lozano-Juste, Jorge; Otani, Masato; Wu, Kevin; Jensen, Davin R; Kollist, Hannes; Volkman, Brian F; Cutler, Sean R

2017-11-17

Increasing drought and diminishing freshwater supplies have stimulated interest in developing small molecules that can be used to control transpiration. Receptors for the plant hormone abscisic acid (ABA) have emerged as key targets for this application, because ABA controls the apertures of stomata, which in turn regulate transpiration. Here, we describe the rational design of cyanabactin, an ABA receptor agonist that preferentially activates Pyrabactin Resistance 1 (PYR1) with low nanomolar potency. A 1.63 Å X-ray crystallographic structure of cyanabactin in complex with PYR1 illustrates that cyanabactin's arylnitrile mimics ABA's cyclohexenone oxygen and engages the tryptophan lock, a key component required to stabilize activated receptors. Further, its sulfonamide and 4-methylbenzyl substructures mimic ABA's carboxylate and C6 methyl groups, respectively. Isothermal titration calorimetry measurements show that cyanabactin's compact structure provides ready access to high ligand efficiency on a relatively simple scaffold. Cyanabactin treatments reduce Arabidopsis whole-plant stomatal conductance and activate multiple ABA responses, demonstrating that its in vitro potency translates to ABA-like activity in vivo. Genetic analyses show that the effects of cyanabactin, and the previously identified agonist quinabactin, can be abolished by the genetic removal of PYR1 and PYL1, which form subclade A within the dimeric subfamily III receptors. Thus, cyanabactin is a potent and selective agonist with a wide spectrum of ABA-like activities that defines subfamily IIIA receptors as key target sites for manipulating transpiration.

Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies.

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Schwarz, Erika N; Ruhlman, Tracey A; Weng, Mao-Lun; Khiyami, Mohammad A; Sabir, Jamal S M; Hajarah, Nahid H; Alharbi, Njud S; Rabah, Samar O; Jansen, Robert K

2017-04-01

This study represents the most comprehensive plastome-wide comparison of nucleotide substitution rates across the three subfamilies of Fabaceae: Caesalpinioideae, Mimosoideae, and Papilionoideae. Caesalpinioid and mimosoid legumes have large, unrearranged plastomes compared with papilionoids, which exhibit varying levels of rearrangement including the loss of the inverted repeat (IR) in the IR-lacking clade (IRLC). Using 71 genes common to 39 legume taxa representing all the three subfamilies, we show that papilionoids consistently have higher nucleotide substitution rates than caesalpinioids and mimosoids, and rates in the IRLC papilionoids are generally higher than those in the IR-containing papilionoids. Unsurprisingly, this pattern was significantly correlated with growth habit as most papilionoids are herbaceous, whereas caesalpinioids and mimosoids are largely woody. Both nonsynonymous (dN) and synonymous (dS) substitution rates were also correlated with several biological features including plastome size and plastomic rearrangements such as the number of inversions and indels. In agreement with previous reports, we found that genes in the IR exhibit between three and fourfold reductions in the substitution rates relative to genes within the large single-copy or small single-copy regions. Furthermore, former IR genes in IR-lacking taxa exhibit accelerated rates compared with genes contained in the IR.

Cloning of MASK, a novel member of mammalian germinal center kinase-III subfamily, with apoptosis-inducing properties

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Dan, Ippeita; Ong, Shao-En; Watanabe, Norinobu M

2002-01-01

We have cloned a novel human GCK family kinase that has been designated as MASK (Mst3 and SOK1-related kinase). MASK is widely expressed and encodes a protein of 416 amino acid residues, with an N-terminal kinase domain and a unique C-terminal region. Like other GCK-III subfamily kinases, MASK do...... apoptosis upon overexpression in mammalian cells that is abrogated by CrmA, suggesting involvement of MASK in the apoptotic machinery in mammalian cells. Udgivelsesdato: 2002-Feb-22...

Molecular systematics of selected genera of subfamily mimosoidae-fabaceae

International Nuclear Information System (INIS)

Shinwari, Z.K.; Jamil, K.; Zahra, N.B.

2014-01-01

Family Mimosoidae-Fabaceae is of economic importance to local communities for its medicinal usage. It has commercial value, but the parts sold in the market are difficult to identify on the basis of morphological characters and therefore needs molecular systematics approaches. Hence, the utility of potential DNA barcodes for selected Acacia and Albizia species by using three cpDNA regions rbcL, matK and trnH-psbA was tested in this study. Our study suggests that the rbcL region can be used to identify these species and discriminate among them more effectively than matK and trnH-psbA. The latter regions proved to be less successful in sequencing particularly trnH-psbA. Therefore, rbcL is an improved and efficient tool for species identification of these medicinal plants and may be recommended for a broad series of subfamily Mimosoideae (Family: Fabaceae) plants, making it a potential DNA barcode for these taxa. Sequence data obtained from rbcL and matK also indicated that Acacia and Albizia are polyphyletic. The phylogenetic analysis on the basis of rbcL proved that Acacia nilotica and Acacia nilotica ssp. hemispherica are closely related as they form the sister groups. (author)

The subfamily-specific interaction between Kv2.1 and Kv6.4 subunits is determined by interactions between the N- and C-termini.

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Elke Bocksteins

Full Text Available The "silent" voltage-gated potassium (KvS channel subunit Kv6.4 does not form electrically functional homotetramers at the plasma membrane but assembles with Kv2.1 subunits, generating functional Kv2.1/Kv6.4 heterotetramers. The N-terminal T1 domain determines the subfamily-specific assembly of Kv1-4 subunits by preventing interactions between subunits that belong to different subfamilies. For Kv6.4, yeast-two-hybrid experiments showed an interaction of the Kv6.4 N-terminus with the Kv2.1 N-terminus, but unexpectedly also with the Kv3.1 N-terminus. We confirmed this interaction by Fluorescence Resonance Energy Transfer (FRET and co-immunoprecipitation (co-IP using N-terminal Kv3.1 and Kv6.4 fragments. However, full-length Kv3.1 and Kv6.4 subunits do not form heterotetramers at the plasma membrane. Therefore, additional interactions between the Kv6.4 and Kv2.1 subunits should be important in the Kv2.1/Kv6.4 subfamily-specificity. Using FRET and co-IP approaches with N- and C-terminal fragments we observed that the Kv6.4 C-terminus physically interacts with the Kv2.1 N-terminus but not with the Kv3.1 N-terminus. The N-terminal amino acid sequence CDD which is conserved between Kv2 and KvS subunits appeared to be a key determinant since charge reversals with arginine substitutions abolished the interaction between the N-terminus of Kv2.1 and the C-terminus of both Kv2.1 and Kv6.4. In addition, the Kv6.4(CKv3.1 chimera in which the C-terminus of Kv6.4 was replaced by the corresponding domain of Kv3.1, disrupted the assembly with Kv2.1. These results indicate that the subfamily-specific Kv2.1/Kv6.4 heterotetramerization is determined by interactions between Kv2.1 and Kv6.4 that involve both the N- and C-termini in which the conserved N-terminal CDD sequence plays a key role.

The nuclear receptor gene family in the Pacific oyster, Crassostrea gigas, contains a novel subfamily group.

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Vogeler, Susanne; Galloway, Tamara S; Lyons, Brett P; Bean, Tim P

2014-05-15

Nuclear receptors are a superfamily of transcription factors important in key biological, developmental and reproductive processes. Several of these receptors are ligand- activated and through their ability to bind endogenous and exogenous ligands, are potentially vulnerable to xenobiotics. Molluscs are key ecological species in defining aquatic and terrestrial habitats and are sensitive to xenobiotic compounds in the environment. However, the understanding of nuclear receptor presence, function and xenobiotic disruption in the phylum Mollusca is limited. Here, forty-three nuclear receptor sequences were mined from the genome of the Pacific oyster, Crassostrea gigas. They include members of NR0-NR5 subfamilies, notably lacking any NR6 members. Phylogenetic analyses of the oyster nuclear receptors have been conducted showing the presence of a large novel subfamily group not previously reported, which is named NR1P. Homologues to all previous identified nuclear receptors in other mollusc species have also been determined including the putative heterodimer partner retinoid X receptor, estrogen receptor and estrogen related receptor. C. gigas contains a highly diverse set of nuclear receptors including a novel NR1 group, which provides important information on presence and evolution of this transcription factor superfamily in invertebrates. The Pacific oyster possesses two members of NR3, the sex steroid hormone receptor analogues, of which there are 9 in humans. This provides increasing evidence that steroid ligand specific expansion of this family is deuterostome specific. This new knowledge on divergence and emergence of nuclear receptors in C. gigas provides essential information for studying regulation of molluscan gene expression and the potential effects of xenobiotics.

Phylogenetic and functional characterization of ten P450 genes from the CYP6AE subfamily of Helicoverpa armigera involved in xenobiotic metabolism

DEFF Research Database (Denmark)

Shi, Yu; Wang, Huidong; Liu, Zhi

2018-01-01

450s in this subfamily can metabolise imidacloprid, but with lower efficiency than Bemisia tabaci CYP6CM1vQ. CYP6AE20 had virtually no metabolic competence to these four compounds but could metabolise several model fluorogenic substrates. These results showed the broad substrate spectrum of H...

A novel MSCRAMM sub-family in Coagulase negative staphylococcal species

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Srishtee eArora

2016-04-01

Full Text Available Coagulase negative staphylococci are important opportunistic pathogens. Staphylococcus epidermidis, a coagulase negative staphylococcus, is the third leading cause of nosocomial infections in the US. Surface proteins like Microbial Surface Components Recognizing Adhesive Matrix Molecules (MSCRAMMs are major virulence factors of pathogenic gram positive bacteria. Here, we identified a new chimeric protein; SesJ in S. epidermidis, which represents a prototype of a new subfamily of MSCRAMMs. Structural predictions show that SesJ has structural features characteristic of a MSCRAMM along with a N-Terminal repeat region and an Aspartic acid containing repeat region, features that have not been previously observed in staphylococcal MSCRAMMs but have been found in other surface proteins from gram positive bacteria. We identified and analyzed structural homologs of SesJ in three other coagulase negative staphylococci. These homologs of SesJ have an identical structural organization but varying sequence identities within the domains. Using flow cytometry, we also show that SesJ is expressed constitutively on the surface of a representative S. epidermidis strain, from early exponential to stationary growth phase. Thus SesJ is positioned to interact with protein targets in the environment and play a role in S. epidermidis virulence.

Anatomy of 31 species from Mimosoideae (Leguminosae) subfamily on Venezuela

International Nuclear Information System (INIS)

Leon, H; Williams, J.

2008-01-01

This paper is about the wood anatomy of 31 species, belonging to 17 genera, of the Mimosoideae subfamily (Leguminosae), proceeding from different geographical regions of Venezuela. For each species, one to five individuals were studied. The descriptions were realized according to the IAWA Committee(1989). The studied species may be divided in two groups according to the presence or absence of septate fibers. All species of Inga showed septate fibers, whereas Albizia and Enterolobium included species with septate fibers and also species with non-septate fibers. The quantitative characteristics of the vessels and the width of rays showed sufficient variation as to be considered important characteristics from ataxonomic point of view. The most common parenchyma type was vasicetric, aliform and confluent. In Calliandra laxa, Prosopis juliflora and Zygia longifolia the main parenchyma type was in wide bands; whereas in Cedrelinga cateniformis, the main parenchyma type was thin vasicentric. All species studied, with the exception of Cedrelinga cateniformis, presented prismatic crystals in the parenchymatous axials cells. In spite of finding certain anatomical uniformity, it was possible to elaborate a key for the identification of the studied species.

Molecular characterization of two sub-family specific monoclonal antibodies to meningococcal Factor H binding protein

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C. Lo Passo

2018-04-01

Full Text Available Factor H binding protein (FHbp is a component of two licensed vaccines for prevention of sepsis and meningitis caused by serogroup B meningococci. FHbp binds human Factor H (FH, which contributes to evasion of host immunity and FHbp sequence variants can be classified into two sub-families. Antibodies against FHbp elicit complement-mediated killing and can inhibit recruitment of FH to the bacterial surface. We report epitope mapping studies of two murine IgG mAbs, designated JAR 31 and JAR 36, isolated from a mouse immunized with FHbp in sub-family A, which is present in ∼30–40% of invasive isolates. In the present study, we tested the reactivity of mAbs JAR 31 and JAR 36 with seven natural FHbp sequence variants from different phylogenic groups. We screened bacteriophage-displayed peptide libraries to identify amino acid residues contributing to the JAR 36 epitope. Based on the reactivities of mAbs JAR 31 and JAR 36 with the seven FHbp variants, and the frequent occurrences of aspartate (D and lysine (K residues in the JAR 36-bound phage peptides, we selected six residues in the carboxyl-terminal region of FHbp for replacement with alanine (A. The D201A and K203A substitutions respectively eliminated and decreased binding of mAbs JAR 31 and JAR 36 to FHbp. These substitutions did not affect binding of the control mAb JAR 33 or of human FH. JAR 31 or JAR 36 mediated cooperative complement-mediated bactericidal activity with other anti-FHbp mAbs. The identification of two amino acid residues involved in the epitopes recognized by these anti-FHbp mAbs may contribute to a more complete understanding of the spatial requirements for cooperative anti-FHbp mAb bactericidal activity. Keywords: Biochemistry, Immunology, Microbiology, Molecular biology

Two ways of legumin-precursor processing in conifers. Characterization and evolutionary relationships of Metasequoia cDNAs representing two divergent legumin gene subfamilies.

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Häger, K P; Wind, C

1997-06-15

Subunit monomers and oligomers of crystalloid-type legumins are major components of SDS-soluble fractions from Metasequoia glyptostroboides (Dawn redwood, Taxodiaceae) seed proteins. The subunits are made up of disulfide linked alpha-polypeptides and beta-polypeptides with molecular masses of 33 kDa and 23-25 kDa, respectively. Unusually for legumins, those from Metasequoia are glycosylated and the carbohydrate moieties are residing in the C-terminal region of the respective beta-polypeptides. A Metasequoia endosperm cDNA library has been constructed and legumin-encoding transcripts representing two divergent gene subfamilies have been characterized. Intersubfamily comparisons reveal 75% identity at the amino acid level and the values range from 53-35% when the legumin precursors deduced were compared with those from angiosperms. The predicted sequences together with data from amino acid sequencing prove that post-translational processing of Metasequoia prolegumins is directed to two different processing sites, each of them specific for one of the legumin subfamilies. The sites involved differ in their relative position and in the junction to be cleaved: Metasequoia legumin precursors MgLeg18 and MgLeg26 contain the conventional post-translational Asn-Gly processing site, which is generally regarded as highly conserved. In contrast, the MgLeg4 precursor is lacking this site and post-translational cleavage is directed to an unusual Asn-Thr processing site located in its hypervariable region, causing N-terminal extension of the beta-polypeptide relative to those hitherto known. Evidence is given that the unusual variant of processing also occurs in other conifers. Phylogenetic analysis reveals the precursors concerned as representatives of a distinct legumin subfamily, originating from duplication of an ancestral gene prior to or at the beginning of Taxodiaceae diversification.

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus.

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Figueroa, Alex; McKelvy, Alexander D; Grismer, L Lee; Bell, Charles D; Lailvaux, Simon P

2016-01-01

With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

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McKelvy, Alexander D.; Grismer, L. Lee; Bell, Charles D.; Lailvaux, Simon P.

2016-01-01

Background With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Results Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Conclusion Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes. PMID:27603205

First record of the subfamily Anoplophilinae (Orthoptera: Rhaphidophoridae) from Russia with description of a new species of the genus Alpinanoplophilus Ishikawa, 1993.

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Storozhenko, Sergey Yu

2015-06-17

The subfamily Anoplophilinae (Rhaphidophopridae) is recorded from Russia for the first time. Alpinanoplophilus kurilensis Storozhenko, sp. nov. is described from Kunashir Island. The holotype of the new species is deposited in the Zoological Institute of Russian Academy of Science (St. Petersburg, Russia). A revised key to the species of the genus Alpinanoplophilus Ishikawa, 1993 is provided.

The Exiguobacterium sibiricum 255-15 GtfC Enzyme Represents a Novel Glycoside Hydrolase 70 Subfamily of 4,6-α-Glucanotransferase Enzymes.

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Gangoiti, Joana; Pijning, Tjaard; Dijkhuizen, Lubbert

2016-01-15

The glycoside hydrolase 70 (GH70) family originally was established for glucansucrase enzymes found solely in lactic acid bacteria synthesizing α-glucan polysaccharides from sucrose (e.g., GtfA). In recent years, we have characterized GtfB and related Lactobacillus enzymes as 4,6-α-glucanotransferase enzymes. These GtfB-type enzymes constitute the first GH70 subfamily of enzymes that are unable to act on sucrose as a substrate but are active with maltodextrins and starch, cleave α1→4 linkages, and synthesize linear α1→6-glucan chains. The GtfB disproportionating type of activity results in the conversion of malto-oligosaccharides into isomalto/malto-polysaccharides with a relatively high percentage of α1→6 linkages. This paper reports the identification of the members of a second GH70 subfamily (designated GtfC enzymes) and the characterization of the Exiguobacterium sibiricum 255-15 GtfC enzyme, which is also inactive with sucrose and displays 4,6-α-glucanotransferase activity with malto-oligosaccharides. GtfC differs from GtfB in synthesizing isomalto/malto-oligosaccharides. Biochemically, the GtfB- and GtfC-type enzymes are related, but phylogenetically, they clearly constitute different GH70 subfamilies, displaying only 30% sequence identity. Whereas the GtfB-type enzyme largely has the same domain order as glucansucrases (with α-amylase domains A, B, and C plus domains IV and V), this GtfC-type enzyme differs in the order of these domains and completely lacks domain V. In GtfC, the sequence of conserved regions I to IV of clan GH-H is identical to that in GH13 (I-II-III-IV) but different from that in GH70 (II-III-IV-I because of a circular permutation of the (β/α)8 barrel. The GtfC 4,6-α-glucanotransferase enzymes thus represent structurally and functionally very interesting evolutionary intermediates between α-amylase and glucansucrase enzymes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Molecular phylogeny of moth-specialized spider sub-family Cyrtarachninae, which includes bolas spiders.

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Tanikawa, Akio; Shinkai, Akira; Miyashita, Tadashi

2014-11-01

The evolutionary process of the unique web architectures of spiders of the sub-family Cyrtarachninae, which includes the triangular web weaver, bolas spider, and webless spider, is thought to be derived from reduction of orbicular 'spanning-thread webs' resembling ordinal orb webs. A molecular phylogenetic analysis was conducted to explore this hypothesis using orbicular web spiders Cyrtarachne, Paraplectana, Poecilopachys, triangular web spider Pasilobus, bolas spiders Ordgarius and Mastophora, and webless spider Celaenia. The phylogeny inferred from partial sequences of mt-COI, nuclear 18S-rRNA and 28S-rRNA showed that the common ancestor of these spiders diverged into two clades: a spanning-thread web clade and a bolas or webless clade. This finding suggests that the triangular web evolved by reduction of an orbicular spanning web, but that bolas spiders evolved in the early stage, which does not support the gradual web reduction hypothesis.

Sea snakes in Australian waters (Serpentes: subfamilies Hydrophiinae and Laticaudinae)—a review with an updated identification key

DEFF Research Database (Denmark)

Redsted Rasmussen, Arne; Sanders, Kate Laura; Guinea, Michael L

2014-01-01

Sea snakes (Elapidae, subfamilies Hydrophiinae and Laticaudinae) reach high species richness in the South China Sea and in the Australian region; however, most countries in the two regions still lack up-to-date checklists and identification tools for these snakes. We present an updated reviewed...... checklist and a new complete identification key to sea snakes in Australian waters. The identification key includes 29 species documented and 4 possibly occurring taxa and is based mostly on easy-to-use external characters. We find no evidence for breeding populations of Laticauda in Australian waters...

Expression analysis of two gene subfamilies encoding the plasma membrane H+-ATPase in Nicotiana plumbaginifolia reveals the major transport functions of this enzyme.

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Moriau, L; Michelet, B; Bogaerts, P; Lambert, L; Michel, A; Oufattole, M; Boutry, M

1999-07-01

The plasma membrane H+-ATPase couples ATP hydrolysis to proton transport, thereby establishing the driving force for solute transport across the plasma membrane. In Nicotiana plumbaginifolia, this enzyme is encoded by at least nine pma (plasma membrane H+-ATPase) genes. Four of these are classified into two gene subfamilies, pma1-2-3 and pma4, which are the most highly expressed in plant species. We have isolated genomic clones for pma2 and pma4. Mapping of their transcript 5' end revealed the presence of a long leader that contained small open reading frames, regulatory features typical of other pma genes. The gusA reporter gene was then used to determine the expression of pma2, pma3 and pma4 in N. tabacum. These data, together with those obtained previously for pma1, led to the following conclusions. (i) The four pma-gusA genes were all expressed in root, stem, leaf and flower organs, but each in a cell-type specific manner. Expression in these organs was confirmed at the protein level, using subfamily-specific antibodies. (ii) pma4-gusA was expressed in many cell types and notably in root hair and epidermis, in companion cells, and in guard cells, indicating that in N. plumbaginifolia the same H+-ATPase isoform might be involved in mineral nutrition, phloem loading and control of stomata aperture. (iii) The second gene subfamily is composed, in N. plumbaginifolia, of a single gene (pma4) with a wide expression pattern and, in Arabidopsis thaliana, of three genes (aha1, aha2, aha3), at least two of them having a more restrictive expression pattern. (iv) Some cell types expressed pma2 and pma4 at the same time, which encode H+-ATPases with different enzymatic properties.

iNR-PhysChem: a sequence-based predictor for identifying nuclear receptors and their subfamilies via physical-chemical property matrix.

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Xuan Xiao

Full Text Available Nuclear receptors (NRs form a family of ligand-activated transcription factors that regulate a wide variety of biological processes, such as homeostasis, reproduction, development, and metabolism. Human genome contains 48 genes encoding NRs. These receptors have become one of the most important targets for therapeutic drug development. According to their different action mechanisms or functions, NRs have been classified into seven subfamilies. With the avalanche of protein sequences generated in the postgenomic age, we are facing the following challenging problems. Given an uncharacterized protein sequence, how can we identify whether it is a nuclear receptor? If it is, what subfamily it belongs to? To address these problems, we developed a predictor called iNR-PhysChem in which the protein samples were expressed by a novel mode of pseudo amino acid composition (PseAAC whose components were derived from a physical-chemical matrix via a series of auto-covariance and cross-covariance transformations. It was observed that the overall success rate achieved by iNR-PhysChem was over 98% in identifying NRs or non-NRs, and over 92% in identifying NRs among the following seven subfamilies: NR1--thyroid hormone like, NR2--HNF4-like, NR3--estrogen like, NR4--nerve growth factor IB-like, NR5--fushi tarazu-F1 like, NR6--germ cell nuclear factor like, and NR0--knirps like. These rates were derived by the jackknife tests on a stringent benchmark dataset in which none of protein sequences included has ≥60% pairwise sequence identity to any other in a same subset. As a user-friendly web-server, iNR-PhysChem is freely accessible to the public at either http://www.jci-bioinfo.cn/iNR-PhysChem or http://icpr.jci.edu.cn/bioinfo/iNR-PhysChem. Also a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics involved in developing the predictor. It is anticipated that iNR-PhysChem may

Sobre um novo gênero neotrópico da subfamília Tanypodinae (Diptera, Chironomidae On a new neotropical genus of the subfamily Tanypodinae (Diptera, Chironomidae

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Sebastião José de Oliveira

1992-01-01

Full Text Available A new neotropical genus and a new species of a non-biting midge for the subfamily Tanypodinae from Brazil are described. The new genus is near Tanypus Meigen, 1803 and Procladius Skuse, 1889, but differs of both by wings and male terminalia.

Morphology of dental bones and teeth of selected representatives of the subfamily Anguinae (Squamata, Anguidae); Morfologia dentalnej kosti a zubov vybranych zastupcov podcelade Anguinae (Squamata, Anguinae)

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Dobiasova, K [Univerzita Komenskeho v Bratislave, Prirodovedecka fakulta, Katedra ekologie, 84215 Bratislava (Slovakia)

2012-04-25

The present study is focused on the comparative morphology of dental bones and teeth of all genuses of the subfamily Anguinae. The research did not show any relevant difference, which would serve as the basis for the return use of the original generic names. (authors)

Analysis of Comparative Sequence and Genomic Data to Verify Phylogenetic Relationship and Explore a New Subfamily of Bacterial Lipases.

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Malihe Masomian

Full Text Available Thermostable and organic solvent-tolerant enzymes have significant potential in a wide range of synthetic reactions in industry due to their inherent stability at high temperatures and their ability to endure harsh organic solvents. In this study, a novel gene encoding a true lipase was isolated by construction of a genomic DNA library of thermophilic Aneurinibacillus thermoaerophilus strain HZ into Escherichia coli plasmid vector. Sequence analysis revealed that HZ lipase had 62% identity to putative lipase from Bacillus pseudomycoides. The closely characterized lipases to the HZ lipase gene are from thermostable Bacillus and Geobacillus lipases belonging to the subfamily I.5 with ≤ 57% identity. The amino acid sequence analysis of HZ lipase determined a conserved pentapeptide containing the active serine, GHSMG and a Ca(2+-binding motif, GCYGSD in the enzyme. Protein structure modeling showed that HZ lipase consisted of an α/β hydrolase fold and a lid domain. Protein sequence alignment, conserved regions analysis, clustal distance matrix and amino acid composition illustrated differences between HZ lipase and other thermostable lipases. Phylogenetic analysis revealed that this lipase represented a new subfamily of family I of bacterial true lipases, classified as family I.9. The HZ lipase was expressed under promoter Plac using IPTG and was characterized. The recombinant enzyme showed optimal activity at 65 °C and retained ≥ 97% activity after incubation at 50 °C for 1h. The HZ lipase was stable in various polar and non-polar organic solvents.

Cloning and characterization of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain

DEFF Research Database (Denmark)

Pandey, A.; Dan, I.; Kristiansen, T.Z.

2002-01-01

cloned a novel human PAK family kinase that has been designated as PAK5. PAK5 contains a CDC42/Rac1 interactive binding (CRIB) motif at the N-terminus and a Ste20-like kinase domain at the C-terminus. PAK5 is structurally most related to PAK4 and PAK6 to make up the PAK-II subfamily. We have shown...

Leaf and stem CO/sub 2/ uptake in the three subfamilies of the Cactaceae. [Pereskia aculeata; Pereskia grandifolia; Maihuenia poeppigii; Carnegiea gigantea; Ferocactus acanthodes; Coryphantha vivipara; Mammillaria dioica; Opuntia ficus-inidica; Pereskiopsis porteri; Quiabentia chacoensis; Austrocylindropuntia subulata

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Nobel, P.S.; Hartsock, T.L.

1986-04-01

Net CO/sub 2/ uptake over 24-hour periods was examined for the leaves and for the stems of 11 species of cacti representing all three subfamilies. For Pereskia aculeata, Pereskia grandifolia, and Maihuenia poeppigii (subfamily Pereskioideae), all the net shoot CO/sub 2/ uptake was by the leaves and during the daytime. In contrast, for the leafless species Carnegiea gigantea, Ferocactus acanthodes, Coryphantha vivipara, and Mammillaria dioica (subfamily Cactoideae), all the shoot net CO/sub 2/ uptake was by the stems and at night. Similarly, for leafless Opuntia ficus-indica (subfamily Opuntioideae), all net CO/sub 2/ uptake occurred at night. For leafy members of the Opuntioideae (Pereskiopsis porteri, Quiabentia chacoensis, Austrocylindropuntia subulata), at least 88% of the shoot CO/sub 2/ uptake over 24 hours was by the leaves and some CO/sub 2/ uptake occurred at night. Leaves responded to the instantaneous level of photosynthetically active radiation (PAR) during the daytime, as occurs for C/sub 3/ plants, whereas nocturnal CO/sub 2/ uptake by stems of O. ficus-indica and F. acanthodes responded to the total daily PAR, as occurs for Crassulacean acid metabolism (CAM) plants. Thus, under the well-watered conditions employed, the Pereskioideae behaved as C/sub 3/ plants, the Cactoideae behaved as CAM plants, and the Opuntioideae exhibited characteristics of both pathways.

Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members

DEFF Research Database (Denmark)

Godoy, Andre S.; Pereira, Caroline S.; Ramia, Marina Paglione

2018-01-01

The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of ß-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general a...

Heterogeneous nuclear ribonucleoproteins H, H', and F are members of a ubiquitously expressed subfamily of related but distinct proteins encoded by genes mapping to different chromosomes

DEFF Research Database (Denmark)

Honoré, B; Rasmussen, H H; Vorum, H

1995-01-01

Molecular cDNA cloning, two-dimensional gel immunoblotting, and amino acid microsequencing identified three sequence-unique and distinct proteins that constitute a subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins corresponding to hnRNPs H, H', and F. These proteins share...... epitopes and sequence identity with two other proteins, isoelectric focusing sample spot numbers 2222 (37.6 kDa; pI 6.5) and 2326 (39.5 kDa; pI 6.6), indicating that the subfamily may contain additional members. The identity between hnRNPs H and H' is 96%, between H and F 78%, and between H' and F 75......%, respectively. The three proteins contain three repeats, which we denote quasi-RRMs (qRRMs) since they have a remote similarity to the RNA recognition motif (RRM). The three qRRMs of hnRNP H, with a few additional NH2-terminal amino acids, were constructed by polymerase chain reaction amplification and used...

pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families.

Science.gov (United States)

Suplatov, Dmitry; Kirilin, Eugeny; Arbatsky, Mikhail; Takhaveev, Vakil; Svedas, Vytas

2014-07-01

The new web-server pocketZebra implements the power of bioinformatics and geometry-based structural approaches to identify and rank subfamily-specific binding sites in proteins by functional significance, and select particular positions in the structure that determine selective accommodation of ligands. A new scoring function has been developed to annotate binding sites by the presence of the subfamily-specific positions in diverse protein families. pocketZebra web-server has multiple input modes to meet the needs of users with different experience in bioinformatics. The server provides on-site visualization of the results as well as off-line version of the output in annotated text format and as PyMol sessions ready for structural analysis. pocketZebra can be used to study structure-function relationship and regulation in large protein superfamilies, classify functionally important binding sites and annotate proteins with unknown function. The server can be used to engineer ligand-binding sites and allosteric regulation of enzymes, or implemented in a drug discovery process to search for potential molecular targets and novel selective inhibitors/effectors. The server, documentation and examples are freely available at http://biokinet.belozersky.msu.ru/pocketzebra and there are no login requirements. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Taxonomic Review of the Sword-tailed Cricket Subfamily Trigonidiinae (Orthoptera: Ensifera: Gryllidae from Korea

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Tae-Woo Kim

2013-01-01

Full Text Available The Korean population of the sword-tailed cricket subfamily Trigonidiinae is reviewed for the first time. Four members of the crickets are confirmed based on the examined material, those are Metioche japonica (Ichikawa, 2001, Svistella bifasciata (Shiraki, 1911, Homoeoxipha obliterata (Caudell, 1927 and Natula matsuurai Sugimoto, 2001, each of them belonging to a different genera. Among them, the former two are reconfirmed since earlier records, and latter two are newly recognized genera and species from the far southern provinces Jeollanam-do and Jeju-do Island in Korea. The type locality of both crickets is Japan, and are also only previously referred to in Japan, but their distributional ranges include neighboring South Korea. A key to the species, descriptions, photographs, figures, and oscillograms of male’s calling sounds are provided to aid their identification.

Unusual evolutionary conservation and further species-specific adaptations of a large family of nonclassical MHC class Ib genes across different degrees of genome ploidy in the amphibian subfamily Xenopodinae.

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Edholm, Eva-Stina; Goyos, Ana; Taran, Joseph; De Jesús Andino, Francisco; Ohta, Yuko; Robert, Jacques

2014-06-01

Nonclassical MHC class Ib (class Ib) genes are a family of highly diverse and rapidly evolving genes wherein gene numbers, organization, and expression markedly differ even among closely related species rendering class Ib phylogeny difficult to establish. Whereas among mammals there are few unambiguous class Ib gene orthologs, different amphibian species belonging to the anuran subfamily Xenopodinae exhibit an unusually high degree of conservation among multiple class Ib gene lineages. Comparative genomic analysis of class Ib gene loci of two divergent (~65 million years) Xenopodinae subfamily members Xenopus laevis (allotetraploid) and Xenopus tropicalis (diploid) shows that both species possess a large cluster of class Ib genes denoted as Xenopus/Silurana nonclassical (XNC/SNC). Our study reveals two distinct phylogenetic patterns among these genes: some gene lineages display a high degree of flexibility, as demonstrated by species-specific expansion and contractions, whereas other class Ib gene lineages have been maintained as monogenic subfamilies with very few changes in their nucleotide sequence across divergent species. In this second category, we further investigated the XNC/SNC10 gene lineage that in X. laevis is required for the development of a distinct semi-invariant T cell population. We report compelling evidence of the remarkable high degree of conservation of this gene lineage that is present in all 12 species of the Xenopodinae examined, including species with different degrees of ploidy ranging from 2, 4, 8 to 12 N. This suggests that the critical role of XNC10 during early T cell development is conserved in amphibians.

Sonorensin: an antimicrobial peptide, belonging to the heterocycloanthracin subfamily of bacteriocins, from a new marine isolate, Bacillus sonorensis MT93.

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Chopra, Lipsy; Singh, Gurdeep; Choudhary, Vikas; Sahoo, Debendra K

2014-05-01

Marine environments are the greatest fronts of biodiversity, representing a resource of unexploited or unknown microorganisms and new substances having potential applications. Among microbial products, antimicrobial peptides (AMPs) have received great attention recently due to their applications as food preservatives and therapeutic agents. A new marine soil isolate producing an AMP was identified as Bacillus sonorensis based on 16S rRNA gene sequence analysis. It produced an AMP that showed a broad spectrum of activity against both Gram-positive and Gram-negative bacteria. The peptide, named sonorensin, was purified to homogeneity using a combination of chromatographic techniques. The intact molecular mass of the purified peptide, 6,274 Da, as revealed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF), was in agreement with Tricine-SDS-PAGE analysis. A PCR array of primers was used to identify AMP structural genes, which allowed the successful amplification of the related genes from strain MT93. The putative open reading frame of sonorensin was amplified, cloned into the pET-32a(+) vector, expressed as a thioredoxin (Trx) fusion protein in Escherichia coli, and then purified. Sequence alignment analysis revealed that the bacteriocin being reported could belong to new subfamily of bacteriocins, heterocycloanthracin. The peptide indicated its potential as a biocontrol agent or food antimicrobial agent, due to its antimicrobial activity against bacteria such as Listeria monocytogenes and Staphylococcus aureus. This is the first report of the production, purification, and characterization of wild-type and recombinant bacteriocin by B. sonorensis and the first bacteriocin of the heterocycloanthracin subfamily to be characterized.

Out of Africa:Miocene Dispersal, Vicariance, and Extinction within Hyacinthaceae Subfamily Urgineoideae

Institute of Scientific and Technical Information of China (English)

Syed Shujait Ali; Martin Pfosser; Wolfgang Wetschnig; Mario MartnezAzorn; Manuel B. Crespo; Yan Yu

2013-01-01

Disjunct distribution patterns in plant lineages are usually explained according to three hypotheses:vicariance, geodispersal, and long-distance dispersal. The role of these hypotheses is tested in Urgineoideae (Hyacinthaceae), a subfamily disjunctly distributed in Africa, Madagascar, India, and the Mediterranean region. The potential ancestral range, dispersal routes, and factors responsible for the current distribution in Urgineoideae are investigated using divergence time estimations. Urgineoideae originated in Southern Africa approximately 48.9 Mya. Two independent dispersal events in the Western Mediterranean region possibly occurred during Early Oligocene and Miocene (29.9-8.5 Mya) via Eastern and Northwestern Africa. A dispersal from Northwestern Africa to India could have occurred between 16.3 and 7.6 Mya. Vicariance and extinction events occurred approximately 21.6 Mya. Colonization of Madagascar occurred between 30.6 and 16.6 Mya, after a single transoceanic dispersal event from Southern Africa. The current disjunct distributions of Urgineoideae are not satisfactorily explained by Gondwana fragmentation or dispersal via boreotropical forests, due to the younger divergence time estimates. The flattened winged seeds of Urgineoideae could have played an important role in long-distance dispersal by strong winds and big storms, whereas geodispersal could have also occurred from Southern Africa to Asia and the Mediterranean region via the so-called arid and high-altitude corridors.

Genome-wide identification of nuclear receptor (NR) genes and the evolutionary significance of the NR1O subfamily in the monogonont rotifer Brachionus spp.

Science.gov (United States)

Kim, Duck-Hyun; Kim, Hui-Su; Hwang, Dae-Sik; Kim, Hee-Jin; Hagiwara, Atsushi; Lee, Jae-Seong; Jeong, Chang-Bum

2017-10-01

Nuclear receptors (NRs) are a large family of transcription factors that are involved in many fundamental biological processes. NRs are considered to have originated from a common ancestor, and are highly conserved throughout the whole animal taxa. Therefore, the genome-wide identification of NR genes in an animal taxon can provide insight into the evolutionary tendencies of NRs. Here, we identified all the NR genes in the monogonont rotifer Brachionus spp., which are considered an ecologically key species due to their abundance and world-wide distribution. The NR family was composed of 40, 32, 29, and 32 genes in the genomes of the rotifers B. calyciflorus, B. koreanus, B. plicatilis, and B. rotundiformis, respectively, which were classified into seven distinct subfamilies. The composition of each subfamily was highly conserved between species, except for NR1O genes, suggesting that they have undergone sporadic evolutionary processes for adaptation to their different environmental pressures. In addition, despite the dynamics of NR evolution, the significance of the conserved endocrine system, particularly for estrogen receptor (ER)-signaling, in rotifers was discussed on the basis of phylogenetic analyses. The results of this study may help provide a better understanding the evolution of NRs, and expand our knowledge of rotifer endocrine systems. Copyright © 2017 Elsevier Inc. All rights reserved.

On the entomofauna of Mt. Durmitor (Northern Montenegro: Braconid wasps of the subfamily Opiinae (Braconidae, Hymenoptera

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Brajković M.M.

2005-01-01

Full Text Available Braconids are primary parasites of other insects and their eggs, larvae, and adults, and species have been recently discovered that lay their eggs in plant seeds. Classified into about 25 genera, more than 1,400 species of Opiinae are known at the present time in the world fauna. They have been registered in all zoogeographic regions. The Opiinae are solitary endoparasites of the larvae of cyclorhaphous Diptera, most often those of species belonging to the families Agromyzidae, Tephritidae, Anthomyiidae Ephydridae. In investigations conducted on Mt. Durmitor since 1982, we have up to now established 10 species of braconids of the subfamily Opiinae (Opius peterseni Fi., O. caudatus Wesm., O. parvungula Th., O. levisWesm., O. pallipesWesm., O. quasiquisti Fi., O. exilis Hal., O. filicornis Th., O. lugens Hal., and O. meracus Fi, eight of which are new for the fauna of Serbia and Montenegro.

Functional diversity for biomass deconstruction in family 5 subfamily 5 (GH5_5) of fungal endo-β1,4-glucanases.

Science.gov (United States)

Li, Bingyao; Walton, Jonathan D

2017-05-01

Endo-β1,4-glucanases in glycosyl hydrolase family 5 (GH5) are ubiquitous enzymes in the multicellular fungi and are common components of enzyme cocktails for biomass conversion. We recently showed that an endo-glucanase of subfamily 5 of GH5 (GH5_5) from Sporotrichum thermophile (StCel5A) was more effective at releasing glucose from pretreated corn stover, when part of an eight-component synthetic enzyme mixture, compared to its closely related counterpart from Trichoderma reesei, TrCel5A. StCel5A and TrCel5A belong to different clades of GH5_5 (GH5_5_1 and GH5_5_2, respectively). To test whether the superior activity of StCel5A was a general property of all enzymes in the GH5_5_2 clade, StCel5A, TrCel5A, and two additional members of each subfamily were expressed in a common host that had been engineered to suppress its native cellulases (T. reesei Δxyr1) and compared against each other alone on pure substrates, in synthetic mixtures on pure substrates, and against each other in synthetic mixtures on real biomass. The results indicated that superiority is a unique property of StCel5A and not of GH5_5_2 generally. The six Cel5A enzymes had significant differences in relative activities on different substrates, in specific activities, and in sensitivities to mannan inhibition. Importantly, the behavior of the six endo-glucanases on pure cellulose substrates did not predict their behavior in combination with other cellulolytic enzymes on a real lignocellulosic biomass substrate.

Crusticorallina gen. nov., a nongeniculate genus in the subfamily Corallinoideae (Corallinales, Rhodophyta).

Science.gov (United States)

Hind, Katharine R; Gabrielson, Paul W; P Jensen, Cassandra; Martone, Patrick T

2016-12-01

Molecular phylogenetic analyses of 18S rDNA (SSU) gene sequences confirm the placement of Crusticorallina gen. nov. in Corallinoideae, the first nongeniculate genus in an otherwise geniculate subfamily. Crusticorallina is distinguished from all other coralline genera by the following suite of morpho-anatomical characters: (i) sunken, uniporate gametangial and bi/tetrasporangial conceptacles, (ii) cells linked by cell fusions, not secondary pit connections, (iii) an epithallus of 1 or 2 cell layers, (iv) a hypothallus that occupies 50% or more of the total thallus thickness, (v) elongate meristematic cells, and (vi) trichocytes absent. Four species are recognized based on rbcL, psbA and COI-5P sequences, C. painei sp. nov., the generitype, C. adhaerens sp. nov., C. nootkana sp. nov. and C. muricata comb. nov., previously known as Pseudolithophyllum muricatum. Type material of Lithophyllum muricatum, basionym of C. muricata, in TRH comprises at least two taxa, and therefore we accept the previously designated lectotype specimen in UC that we sequenced to confirm its identity. Crusticorallina species are very difficult to distinguish using morpho-anatomical and/or habitat characters, although at specific sites, some species may be distinguished by a combination of morpho-anatomy, habitat and biogeography. The Northeast Pacific now boasts six coralline endemic genera, far more than any other region of the world. © 2016 Phycological Society of America.

Synopsis Of The subfamily Spiranthoideae (Orchidaceae) In Colombia, Part II

International Nuclear Information System (INIS)

Duenas Gomez, Hilda del Carmen; Fernandez Alonso, Jose Luis

2009-01-01

As second and last contribution to the synoptic treatment of the Spiranthoideae for Colombia, the synopsis of the tribes Spirantheae (subtribes Cyclopogoninae: 3 genera, 41 species and Stenorrhynchidinae: 9 genera, 15 species) and Cranichideae (5 genera, 53 species), is presented. The most diverse genera in these tribes are: Cranichis (20 species), Cyclopogon (17), Ponthieva (15) and Pelexia (14). As part of the results of this study: a)- The transfer of Cybebus from the subtribe Spiranthinae (where it was commonly placed) to the subtribe Stenorhinchidinae, is proposed, based on the floral morphology (the rostellum and viscidium structure). b)- two genera are reported for Colombia as new records, each one with one species: Lyroglossa (L. grisebachii) and Helonoma; for the latter the new combination Helonoma peruviana (Szlach.) Salazar, Duenas and Fern. Alonso is proposed. c) New records in the previously known list of Colombian orchids are presented: Coccineorchis (C. cristata, C. navarrensis), Cyclopogon (C. maldonadoanus, C. olivaceus, C. rimbachii), Pelexia (P. hirta, P. palmorchidis), Ponthieva (P. venusta), and Sarcoglottis (S. grandiflora, S. maasorum, S. neglecta, S. stergiosii). d)- And additional 19 new records of species belonging to Aspidogyne and Microchilus, not reported in Duenas and Fernandez-Alonso (2007), are also included. e)- Finally an analysis of the distribution and diversity of the genera of this subfamily, according to altitude ranges in Colombia is presented. This group has predominant Andean distribution, being found mainly between 1300 and 3600 m of altitude. Genera broadly distributed as Microchilus, Gomphichis, Cyclopogon, Pelexia, Sarcoglottis, Coccineorchis, Stenorrhynchos, Cranichis and Ponthieva, are found almost from the level up to 3000 m, in all the regions of the country. In contrast, Beloglottis, Brachystele, Cybebus, Eltroplectris, Hapalorchis, Helonoma, Lankesterella, Lyroglossa, Kreodanthus, Pteroglossa and Sauroglossum

Phylogenetic analysis of the spider mite sub-family Tetranychinae (Acari: Tetranychidae based on the mitochondrial COI gene and the 18S and the 5' end of the 28S rRNA genes indicates that several genera are polyphyletic.

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Tomoko Matsuda

Full Text Available The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825-1,901 bp and 28S (the 5' end of 646-743 bp rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp. As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.

Submission to GenBank of the Plasma membrane intrinsic protein (PIP) Subfamily in Cotton – GenBank Accession No. GU998827-GU998830 and GenBank Accession TPA;inferential No. BK007045-BK007052

Science.gov (United States)

The plasma membrane intrinsic proteins (PIP) are one of the five aquaporin protein subfamilies. Aquaporin proteins are known to facilitate water transport through biological membranes. In order to identify NIP aquaporin gene candidates in cotton (Gossypium hirsutum L.), in silico and molecular clon...

Crystal Structure of Perakine Reductase, Founding Member of a Novel Aldo-Keto Reductase (AKR) Subfamily That Undergoes Unique Conformational Changes during NADPH Binding*

Science.gov (United States)

Sun, Lianli; Chen, Yixin; Rajendran, Chitra; Mueller, Uwe; Panjikar, Santosh; Wang, Meitian; Mindnich, Rebekka; Rosenthal, Cindy; Penning, Trevor M.; Stöckigt, Joachim

2012-01-01

Perakine reductase (PR) catalyzes the NADPH-dependent reduction of the aldehyde perakine to yield the alcohol raucaffrinoline in the biosynthetic pathway of ajmaline in Rauvolfia, a key step in indole alkaloid biosynthesis. Sequence alignment shows that PR is the founder of the new AKR13D subfamily and is designated AKR13D1. The x-ray structure of methylated His6-PR was solved to 2.31 Å. However, the active site of PR was blocked by the connected parts of the neighbor symmetric molecule in the crystal. To break the interactions and obtain the enzyme-ligand complexes, the A213W mutant was generated. The atomic structure of His6-PR-A213W complex with NADPH was determined at 1.77 Å. Overall, PR folds in an unusual α8/β6 barrel that has not been observed in any other AKR protein to date. NADPH binds in an extended pocket, but the nicotinamide riboside moiety is disordered. Upon NADPH binding, dramatic conformational changes and movements were observed: two additional β-strands in the C terminus become ordered to form one α-helix, and a movement of up to 24 Å occurs. This conformational change creates a large space that allows the binding of substrates of variable size for PR and enhances the enzyme activity; as a result cooperative kinetics are observed as NADPH is varied. As the founding member of the new AKR13D subfamily, PR also provides a structural template and model of cofactor binding for the AKR13 family. PMID:22334702

The effects of IL-20 subfamily cytokines on reconstituted human epidermis suggest potential roles in cutaneous innate defense and pathogenic adaptive immunity in psoriasis.

Science.gov (United States)

Sa, Susan M; Valdez, Patricia A; Wu, Jianfeng; Jung, Kenneth; Zhong, Fiona; Hall, Linda; Kasman, Ian; Winer, Jane; Modrusan, Zora; Danilenko, Dimitry M; Ouyang, Wenjun

2007-02-15

IL-19, IL-20, IL-22, IL-24, and IL-26 are members of the IL-10 family of cytokines that have been shown to be up-regulated in psoriatic skin. Contrary to IL-10, these cytokines signal using receptor complex R1 subunits that are preferentially expressed on cells of epithelial origin; thus, we henceforth refer to them as the IL-20 subfamily cytokines. In this study, we show that primary human keratinocytes (KCs) express receptors for these cytokines and that IL-19, IL-20, IL-22, and IL-24 induce acanthosis in reconstituted human epidermis (RHE) in a dose-dependent manner. These cytokines also induce expression of the psoriasis-associated protein S100A7 and keratin 16 in RHE and cause persistent activation of Stat3 with nuclear localization. IL-22 had the most pronounced effects on KC proliferation and on the differentiation of KCs in RHE, inducing a decrease in the granular cell layer (hypogranulosis). Furthermore, gene expression analysis performed on cultured RHE treated with these cytokines showed that IL-19, IL-20, IL-22, and IL-24 regulate many of these same genes to variable degrees, inducing a gene expression profile consistent with inflammatory responses, wound healing re-epithelialization, and altered differentiation. Many of these genes have also been found to be up-regulated in psoriatic skin, including several chemokines, beta-defensins, S100 family proteins, and kallikreins. These results confirm that IL-20 subfamily cytokines are important regulators of epidermal KC biology with potentially pivotal roles in the immunopathology of psoriasis.

Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transporter Subfamily A Protein.

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Wee Tek Tay

2015-11-01

Full Text Available The use of conventional chemical insecticides and bacterial toxins to control lepidopteran pests of global agriculture has imposed significant selection pressure leading to the rapid evolution of insecticide resistance. Transgenic crops (e.g., cotton expressing the Bt Cry toxins are now used world wide to control these pests, including the highly polyphagous and invasive cotton bollworm Helicoverpa armigera. Since 2004, the Cry2Ab toxin has become widely used for controlling H. armigera, often used in combination with Cry1Ac to delay resistance evolution. Isolation of H. armigera and H. punctigera individuals heterozygous for Cry2Ab resistance in 2002 and 2004, respectively, allowed aspects of Cry2Ab resistance (level, fitness costs, genetic dominance, complementation tests to be characterised in both species. However, the gene identity and genetic changes conferring this resistance were unknown, as was the detailed Cry2Ab mode of action. No cross-resistance to Cry1Ac was observed in mutant lines. Biphasic linkage analysis of a Cry2Ab-resistant H. armigera family followed by exon-primed intron-crossing (EPIC marker mapping and candidate gene sequencing identified three independent resistance-associated INDEL mutations in an ATP-Binding Cassette (ABC transporter gene we named HaABCA2. A deletion mutation was also identified in the H. punctigera homolog from the resistant line. All mutations truncate the ABCA2 protein. Isolation of further Cry2Ab resistance alleles in the same gene from field H. armigera populations indicates unequal resistance allele frequencies and the potential for Bt resistance evolution. Identification of the gene involved in resistance as an ABC transporter of the A subfamily adds to the body of evidence on the crucial role this gene family plays in the mode of action of the Bt Cry toxins. The structural differences between the ABCA2, and that of the C subfamily required for Cry1Ac toxicity, indicate differences in the

Revision of Drusinae subfamily (Trichoptera, Limnephilidae: divergence by paraproct and paramere: speciation in isolation by integration

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Oláh, János

2017-08-01

Full Text Available In the last few years we have described over 70 new incipient sibling limnephild species applying the discovered Trichoptera speciation traits of the paraproct and paramere for species recognition and delimitation. In this revision on Drusinae subfamily, comprising 177 species, we have applied these subtle, but rapid and stable speciation traits and described 49 new sibling species from the “well studied” European mountain ranges. Discussing the theoretical background we have elaborated and adapted a new character state ranking system of phenomics to revise the long-neglected taxonomy of the Drusinae subfamily and synonymised the Cryptothrix, Monocentra, Metanoea, Leptodrusus, Anomalopterygella, Hadimina genera with the Drusus genus. These old genera of artificial constructs were established exclusively by divergences of secondary sexual traits known already to have only species level ranking value. According to our new character ranking system in the Drusinae subfamily, beside the Drusus genus, only the Ecclisopteryx genus has been retained having robust generic level divegences of paraproct loss and ancestral duplication of spine organising centre on the paramere pattern. Speciation trait function of the peg-packed surface on the paraproct head in Drusus genus moved to the gonopod apices and integrated into variously shaped stimulatory organ in the Ecclisopteryx genus. In the Drusus genus the ancestral divergence of the single spine organising centre has integrated 11 species groups with remarkably stable paramere spine pattern. Based upon ancestral divergences in the paraproct architecture we have differenciated 28 species complexes inside the 11 species groups. The delineation of the 163 mostly incipient siblings species, inside the 28 species complexes with 44 new Drusus species, was based primarily on the divergences of speciation trait, that is in the stimulatory head shape of the apical arms on the dorsal branches of the paraproct

Paralog-divergent Features May Help Reduce Off-target Effects of Drugs: Hints from Glucagon Subfamily Analysis

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Zhining Sa

2017-08-01

Full Text Available Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To identify targetable differences between paralogs, we analyzed two types (type-I and type-II of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors (GPCRs at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor (GCGR and glucagon-like peptide-1 receptor (GLP-1R, exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes. Our data showed that type-II amino acids were significantly enriched in the binding sites of antagonist MK-0893 to GCGR, which had a radical shift in physicochemical properties between GCGR and GLP-1R. We also examined the role of type-I amino acids between GCGR and GLP-1R. The divergent features between GCGR and GLP-1R paralogs may be helpful in their discrimination, thus enabling the identification of binding sites to reduce undesirable side effects and increase the target specificity of drugs.

Species-specific evolution of class I MHC genes in iguanas (order: Squamata; subfamily: Iguaninae).

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Glaberman, Scott; Caccone, Adalgisa

2008-07-01

Over the last few decades, the major histocompatibility complex (MHC) has emerged as a model for understanding the influence of natural selection on genetic diversity in populations as well as for investigating the genetic basis of host resistance to pathogens. However, many vertebrate taxa remain underrepresented in the field of MHC research, preventing its application to studies of disease, evolution, and conservation genetics in these groups. This is particularly true for squamates, which are by far the most diversified order of non-avian reptiles but have not been the subject of any recent MHC studies. In this paper, we present MHC class I complementary DNA data from three squamate species in the subfamily Iguaninae (iguanas): the Galápagos marine iguana (Amblyrhynchus cristatus), the Galápagos land iguana (Conolophus subcristatus), and the green iguana (Iguana iguana). All sequences obtained are related to the few published class I genes from other squamates. There is evidence for multiple loci in each species, and the conserved alpha-3 domain appears to be evolving in a species-specific manner. Conversely, there is some indication of shared polymorphism between species in the peptide-binding alpha-1 and alpha-2 domains, suggesting that these two regions have different phylogenetic histories. The great similarity between alpha-3 sequences in marine iguanas in particular suggests that concerted evolution is acting to homogenize class I loci within species. However, while less likely, the data are also compatible with a birth and death model of evolution.

Regulation of protease-activated receptor 1 signaling by the adaptor protein complex 2 and R4 subfamily of regulator of G protein signaling proteins.

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Chen, Buxin; Siderovski, David P; Neubig, Richard R; Lawson, Mark A; Trejo, Joann

2014-01-17

The G protein-coupled protease-activated receptor 1 (PAR1) is irreversibly proteolytically activated by thrombin. Hence, the precise regulation of PAR1 signaling is important for proper cellular responses. In addition to desensitization, internalization and lysosomal sorting of activated PAR1 are critical for the termination of signaling. Unlike most G protein-coupled receptors, PAR1 internalization is mediated by the clathrin adaptor protein complex 2 (AP-2) and epsin-1, rather than β-arrestins. However, the function of AP-2 and epsin-1 in the regulation of PAR1 signaling is not known. Here, we report that AP-2, and not epsin-1, regulates activated PAR1-stimulated phosphoinositide hydrolysis via two different mechanisms that involve, in part, a subset of R4 subfamily of "regulator of G protein signaling" (RGS) proteins. A significantly greater increase in activated PAR1 signaling was observed in cells depleted of AP-2 using siRNA or in cells expressing a PAR1 (420)AKKAA(424) mutant with defective AP-2 binding. This effect was attributed to AP-2 modulation of PAR1 surface expression and efficiency of G protein coupling. We further found that ectopic expression of R4 subfamily members RGS2, RGS3, RGS4, and RGS5 reduced activated PAR1 wild-type signaling, whereas signaling by the PAR1 AKKAA mutant was minimally affected. Intriguingly, siRNA-mediated depletion analysis revealed a function for RGS5 in the regulation of signaling by the PAR1 wild type but not the AKKAA mutant. Moreover, activation of the PAR1 wild type, and not the AKKAA mutant, induced Gαq association with RGS3 via an AP-2-dependent mechanism. Thus, AP-2 regulates activated PAR1 signaling by altering receptor surface expression and through recruitment of RGS proteins.

Low dose trichloroethylene alters cytochrome P450 - 2C subfamily expression in the developing chick heart

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Makwana, Om; Ahles, Lauren; Lencinas, Alejandro; Selmin, Ornella I.; Runyan, Raymond B.

2013-01-01

Trichloroethylene (TCE) is an organic solvent and common environmental contaminant. TCE exposure is associated with heart defects in humans and animal models. Primary metabolism of TCE in adult rodent models is by specific hepatic cytochrome P450 enzymes (Lash et al., 2000). As association of TCE exposure with cardiac defects is in exposed embryos prior to normal liver development, we investigated metabolism of TCE in the early embryo. Developing chick embryos were dosed in ovo with environmentally relevant doses of TCE (8 ppb and 800 ppb) and RNA was extracted from cardiac and extra-cardiac tissue (whole embryo without heart). Real time PCR showed upregulation of CYP2H1 transcripts in response to TCE exposure in the heart. No detectable cytochrome expression was found in extra-cardiac tissue. As seen previously, the dose response was non-monotonic and 8ppb elicited stronger upregulation than 800 ppb. Immunostaining for CYP2C subfamily expression confirmed protein expression and showed localization in both myocardium and endothelium. TCE exposure increased protein expression in both tissues. These data demonstrate that the earliest embryonic expression of phase I detoxification enzymes is in the developing heart. Expression of these CYPs is likely to be relevant to the susceptibility of the developing heart to environmental teratogens. PMID:22855351

Markiana nigripinnis (Perugia, 1891 as a putative member of the subfamily Stevardiinae (Characiformes: Characidae: spermatic evidence

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Clarianna Martins Baicere-Silva

Full Text Available The genus Markiana was until recently recognized as incertae sedis in the family Characidae, even though alternative placements for this genus have been advanced since its original description. More recently, it was hypothesized that Markiana nigripinnis is part of a clade informally named the Astyanax clade, indicating the putative close relationship of Markiana with the genus Astyanax. Examination of sperm ultrastructure of representatives of Astyanax and M. nigripinnis shows no evidence for this hypothesized close relationship. Rather, the spermatozoa of M. nigripinnis share characters found in spermatozoa of the non-inseminating members of the subfamily Stevardiinae, such as an angle of nuclear rotation equal to 85º resulting in a lateral position of the double nuclear fossa and flagellum. As with the non-inseminating Stevardiinae, sperm nuclei are also slightly elongate toward the flagellum, the proximal centriole is partially inside the nuclear fossa and anterior and oblique to the distal centriole, and the midpiece is short and strongly asymmetric. Additionally, M. nigripinnis shares with the other members of the Stevardiinae the presence of only four teeth in the inner row of the premaxillary and a short triangular ectopterygoid, which is never more than twice the length of the palatine.

A new species of Glaphyropoma: the first subterranean copionodontine catfish and the first occurrence of opercular odontodes in the subfamily (Siluriformes: Trichomycteridae

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Maria Elina Bichuette

Full Text Available A new species of the rare copionodontine genus Glaphyropoma is described from subterranean waters in the Diamantina Plateau, Bahia State, central northeastern Brazil. This is the first troglomorphic species in the subfamily Copionodontinae. It is distinguished from all other copionodontines by the presence of opercular odontodes, and further distinguished from its only congener, G. rodriguesi, by the reduction of dark integumentary pigmentation. The new species shares the single synapomorphy previously proposed for Glaphyropoma, the marked narrowing of the first hypobranchial and indirect character evidence also supports its inclusion in the genus. The presence of opercular odontodes in the new species, in combination with a reviewed hypothesis of sister group relationship between Copionodontinae and Trichogeninae, indicate that the absence of opercular odontodes in previously-known copionodontines is secondary, rather than primitive.

Comparative anatomy of the cheek muscles within the Centromochlinae subfamily (Ostariophysi, Siluriformes, Auchenipteridae).

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Sarmento-Soares, Luisa Maria; Porto, Marcovan

2006-02-01

Glanidium melanopterum Miranda Ribeiro, a typical representative of the subfamily Centromochlinae (Siluriformes: Auchenipteridae), is herein described myologically and compared to other representative species within the group, Glanidium ribeiroi, G. leopardum, Tatia neivai, T. intermedia, T. creutzbergi, Centromochlus heckelii, and C. existimatus. The structure of seven pairs of striated cephalic muscles was compared anatomically: adductor mandibulae, levator arcus palatini, dilatator operculi, adductor arcus palatini, extensor tentaculi, retractor tentaculi, and levator operculi. We observed broad adductor mandibulae muscles in both Glanidium and Tatia, catfishes with depressed heads and smaller eyes. Similarities between muscles were observed: the presence of a large aponeurotic insertion for the levator arcus palatini muscle; an adductor arcus palatini muscle whose origin spread over the orbitosphenoid, pterosphenoid, and parasphenoid; and the extensor tentaculi muscle broadly attached to the autopalatine. There is no retractor tentaculi muscle in either the Glanidium or Tatia species. On the other hand, in Centromochlus, with forms having large eyes and the tallest head, the adductor mandibulae muscles are slim; there is a thin aponeurotic or muscular insertion for the levator arcus palatini muscle; the adductor arcus palatini muscle originates from a single osseous process, forming a keel on the parasphenoid; the extensor tentaculi muscle is loosely attached to the autopalatine, permitting exclusive rotating and sliding movements between this bone and the maxillary. The retractor tentaculi muscle is connected to the maxilla through a single tendon, so that both extensor and retractor tentaculi muscles contribute to a wide array of movements of the maxillary barbels. A discussion on the differences in autopalatine-maxillary movements among the analyzed groups is given. (c) 2005 Wiley-Liss, Inc.

Key to the subfamilies, tribes and genera of adult Dytiscidae of Argentina (Coleoptera: Adephaga Clave para los adultos de las subfamilias, tribus y géneros de Dytiscidae de la Argentina (Coleoptera: Adephaga

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María L. Libonatti

2011-12-01

Full Text Available Dytiscids constitute the world's most speciose family of water beetles, whose identifi cation in Argentina is problematic with current keys. In this work, a key (both in English and Spanish to the eight subfamilies, 16 tribes and 31 genera of adult Dytiscidae of Argentina is presented. The key was constructed using stable qualitative characters of the external morphology and chaetotaxy, easily visualizable and interpretable. Characters such as size and shape of the body, color pattern and geographic distribution were also used. Illustrations of a great number of morphological structures as well as SEM micrographs were included to aid in the interpretation of the text. One subfamily (Hydrodytinae and fi ve genera (Agaporomorphus Zimmermann, Bidessodes Régimbart, Hydrodytes Miller, Queda Sharp and an unpublished genus of the subfamily Laccophilinae are cited for the fi rst time for Argentina.Los ditíscidos constituyen la familia más numerosa de escarabajos acuáticos a nivel mundial, cuya identifi cación en la Argentina resulta problemática con las claves actuales. En este trabajo, se presenta una clave (en inglés y español para los adultos de las ocho subfamilias, 16 tribus y 31 géneros de Dytiscidae de la Argentina. La clave fue construida priorizando la inclusión de caracteres cualitativos estables de la morfología externa y quetotaxia, fácilmente visibles e interpretables. También, se utilizaron caracteres como el tamaño y la forma del cuerpo, el patrón de coloración y la distribución geográfi ca. Se incluyeron ilustraciones de un gran número de estructuras morfológicas y fotografías tomadas con el microscopio electrónico, para ayudar a la interpretación del texto. Se citan, por primera vez para la Argentina, una subfamilia (Hydrodytinae y cinco géneros (Agaporomorphus Zimmermann, Bidessodes Régimbart, Hydrodytes Miller, Queda Sharp y un género inédito de la subfamilia Laccophilinae.

Freyinae, a major new subfamily of Neotropical jumping spiders (Araneae: Salticidae).

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Edwards, G B

2015-11-02

Freyinae, new subfamily, is described for a group of genera of Neotropical jumping spiders that can be distinguished from other non-ant mimic salticoid Neotropical salticids by having the following three morphological features: a slightly more elongate carapace, a distinctive prolateral tibial macrosetae arrangement (medially placed subdistal and subproximal macrosetae, with a subdorsal medial macroseta in some males), and an unusual dorsoventrally thick tegulum basal division (although one or two of these features are sometimes lost). It includes 20 genera previously considered valid, of which 19 are retained: Akela Peckham & Peckham, 1896, Aphirape C.L. Koch, 1850, Asaracus C.L. Koch, 1846, Capidava Simon, 1902, Chira Peckham & Peckham, 1896, Edilemma Ruiz & Brescovit, 2006, Eustiromastix Simon, 1902, Freya C.L. Koch, 1850, Frigga C.L. Koch, 1850, Kalcerrytus Galiano, 2000, Nycerella Galiano, 1982, Onofre Ruiz & Brescovit, 2007, Pachomius Peckham & Peckham, 1896, Phiale C.L. Koch, 1846, Rishaschia Makhan, 2006, Sumampattus Galiano, 1983, Trydarssus Galiano, 1995, Tullgrenella Mello‑Leitão, 1941, and Wedoquella Galiano, 1984. Romitia Caporiacco, 1947 (and its synonym Uspachus Galiano, 1995) is synonymized with Pachomius, new synonymy. New genera described in the subfamily are: Drizztius, Leptofreya, Megafreya, Philira, Tarkas, Triggella, and Xanthofreya. The following nomenclatorial changes are made: New synonyms: Freya demarcata Chamberlin & Ivie, 1936 = Freya (sub Cyrene) albosignata (F.O.P.-Cambridge, 1901); Freya (sub Cyrene) grisea (F.O.P.-Cambridge, 1901) = Freya (sub Cyrene) infuscata (F.O.P.-Cambridge, 1901); Freya (sub Cyrene) emarginata (F.O.P.-Cambridge, 1901) and Nycerella (sub Heraclea) sanguinea paradoxa (Peckham & Peckham, 1896) = Nycerella (sub Heraclea) sanguinea (Peckham & Peckham, 1896); Pachomius (sub Phiale) maculosus (Chickering, 1946) = Phiale (sub Cyrene) bilobata (F.O.P.-Cambridge, 1901); Phiale (sub Cyrene) mediocava (F

Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

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Matus, José Tomás; Aquea, Felipe; Arce-Johnson, Patricio

2008-01-01

Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions. PMID:18647406

Identification and Structure-Function Analysis of Subfamily Selective G Protein-Coupled Receptor Kinase Inhibitors

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Homan, Kristoff T.; Larimore, Kelly M.; Elkins, Jonathan M.; Szklarz, Marta; Knapp, Stefan; Tesmer, John J.G. [Michigan; (Oxford)

2015-02-13

Selective inhibitors of individual subfamilies of G protein-coupled receptor kinases (GRKs) would serve as useful chemical probes as well as leads for therapeutic applications ranging from heart failure to Parkinson’s disease. To identify such inhibitors, differential scanning fluorimetry was used to screen a collection of known protein kinase inhibitors that could increase the melting points of the two most ubiquitously expressed GRKs: GRK2 and GRK5. Enzymatic assays on 14 of the most stabilizing hits revealed that three exhibit nanomolar potency of inhibition for individual GRKs, some of which exhibiting orders of magnitude selectivity. Most of the identified compounds can be clustered into two chemical classes: indazole/dihydropyrimidine-containing compounds that are selective for GRK2 and pyrrolopyrimidine-containing compounds that potently inhibit GRK1 and GRK5 but with more modest selectivity. The two most potent inhibitors representing each class, GSK180736A and GSK2163632A, were cocrystallized with GRK2 and GRK1, and their atomic structures were determined to 2.6 and 1.85 Å spacings, respectively. GSK180736A, developed as a Rho-associated, coiled-coil-containing protein kinase inhibitor, binds to GRK2 in a manner analogous to that of paroxetine, whereas GSK2163632A, developed as an insulin-like growth factor 1 receptor inhibitor, occupies a novel region of the GRK active site cleft that could likely be exploited to achieve more selectivity. However, neither compound inhibits GRKs more potently than their initial targets. This data provides the foundation for future efforts to rationally design even more potent and selective GRK inhibitors.

The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters

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Strassmann Joan E

2004-03-01

Full Text Available Abstract Background Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera using 69 species. Results Our phylogeny is largely concordant with previous phylogenies at higher levels, and is more resolved at the species level. Our results support the monophyly of the New World subgenera of Polistini, while the Old World subgenera are a paraphyletic group. All genera for which we had more than one exemplar were supported as monophyletic except Polybia which is not resolved, and may be paraphyletic. Conclusion The combination of DNA sequences from flanks of microsatellite repeats with mtCOI sequences and morphological characters proved to be useful characters establishing relationships among the different subgenera and species of the Polistini. This is the first detailed hypothesis for the species of this important group.

Significant Microsynteny with New Evolutionary Highlights Is Detected through Comparative Genomic Sequence Analysis of Maize CCCH IX Gene Subfamily

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Wei-Jun Chen

2015-01-01

Full Text Available CCCH zinc finger proteins, which are characterized by the presence of three cysteine residues and one histidine residue, play important roles in RNA processing in plants. Subfamily IX CCCH proteins were recently shown to function in stress tolerances. In this study, we analyzed CCCH IX genes in Zea mays, Oryza sativa, and Sorghum bicolor. These genes, which are almost intronless, were divided into four groups based on phylogenetic analysis. Microsynteny analysis revealed microsynteny in regions of some gene pairs, indicating that segmental duplication has played an important role in the expansion of this gene family. In addition, we calculated the dates of duplication by Ks analysis, finding that all microsynteny blocks were formed after the monocot-eudicot divergence. We found that deletions, multiplications, and inversions were shown to have occurred over the course of evolution. Moreover, the Ka/Ks ratios indicated that the genes in these three grass species are under strong purifying selection. Finally, we investigated the evolutionary patterns of some gene pairs conferring tolerance to abiotic stress, laying the foundation for future functional studies of these transcription factors.

The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases

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Tran, Timothy H.; Christoffersen, S.; Allan, Paula W.; Parker, William B.; Piskur, Jure; Serra, I.; Terreni, M.; Ealick, Steven E. (Cornell); (Pavia); (Lund); (Southern Research)

2011-09-20

Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 {angstrom} resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamer with an ?/? monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is {approx}7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.

G Protein-coupled Receptor Kinases of the GRK4 Protein Subfamily Phosphorylate Inactive G Protein-coupled Receptors (GPCRs).

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Li, Lingyong; Homan, Kristoff T; Vishnivetskiy, Sergey A; Manglik, Aashish; Tesmer, John J G; Gurevich, Vsevolod V; Gurevich, Eugenia V

2015-04-24

G protein-coupled receptor (GPCR) kinases (GRKs) play a key role in homologous desensitization of GPCRs. It is widely assumed that most GRKs selectively phosphorylate only active GPCRs. Here, we show that although this seems to be the case for the GRK2/3 subfamily, GRK5/6 effectively phosphorylate inactive forms of several GPCRs, including β2-adrenergic and M2 muscarinic receptors, which are commonly used as representative models for GPCRs. Agonist-independent GPCR phosphorylation cannot be explained by constitutive activity of the receptor or membrane association of the GRK, suggesting that it is an inherent ability of GRK5/6. Importantly, phosphorylation of the inactive β2-adrenergic receptor enhanced its interactions with arrestins. Arrestin-3 was able to discriminate between phosphorylation of the same receptor by GRK2 and GRK5, demonstrating preference for the latter. Arrestin recruitment to inactive phosphorylated GPCRs suggests that not only agonist activation but also the complement of GRKs in the cell regulate formation of the arrestin-receptor complex and thereby G protein-independent signaling. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification.

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Covain, Raphaël; Fisch-Muller, Sonia; Oliveira, Claudio; Mol, Jan H; Montoya-Burgos, Juan I; Dray, Stéphane

2016-01-01

The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria. Copyright © 2015 Elsevier Inc. All rights reserved.

Amphibious shelter-builder Oniscidea species from the New World with description of a new subfamily, a new genus and a new species from Brazilian cave (Isopoda, Synocheta, Styloniscidae).

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Souza, Leila A; Ferreira, Rodrigo L; Senna, André R

2015-01-01

The new subfamily Iuiuniscinae, Styloniscidae, is erected for the new genus Iuiuniscus and the new species I. iuiuensis, which is described from cave of the State of Bahia, Northeastern Brazil. A special ecological character is shown here for the first time for a New World Oniscidea: the construction of mud shelters. An introduction addressing the systematics of Synocheta with emphasis on Styloniscidae Vandel, 1952 is provided, as well as general comments about the dependence of water in some Oniscidea and ecological traits of amphibious Synocheta. The problems referring to nomenclature, taxonomy and the interrelationships in Styloniscidae are discussed.

Amphibious shelter-builder Oniscidea species from the New World with description of a new subfamily, a new genus and a new species from Brazilian cave (Isopoda, Synocheta, Styloniscidae.

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Leila A Souza

Full Text Available The new subfamily Iuiuniscinae, Styloniscidae, is erected for the new genus Iuiuniscus and the new species I. iuiuensis, which is described from cave of the State of Bahia, Northeastern Brazil. A special ecological character is shown here for the first time for a New World Oniscidea: the construction of mud shelters. An introduction addressing the systematics of Synocheta with emphasis on Styloniscidae Vandel, 1952 is provided, as well as general comments about the dependence of water in some Oniscidea and ecological traits of amphibious Synocheta. The problems referring to nomenclature, taxonomy and the interrelationships in Styloniscidae are discussed.

Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

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Arce-Johnson Patricio

2008-07-01

Full Text Available Abstract Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions.

A role for calcium in the regulation of ATP-binding cassette, sub-family C, member 3 (ABCC3) gene expression in a model of epidermal growth factor-mediated breast cancer epithelial-mesenchymal transition.

Science.gov (United States)

Stewart, Teneale A; Azimi, Iman; Thompson, Erik W; Roberts-Thomson, Sarah J; Monteith, Gregory R

2015-03-13

Epithelial-mesenchymal transition (EMT), a process implicated in cancer metastasis, is associated with the transcriptional regulation of members of the ATP-binding cassette superfamily of efflux pumps, and drug resistance in breast cancer cells. Epidermal growth factor (EGF)-induced EMT in MDA-MB-468 breast cancer cells is calcium signal dependent. In this study induction of EMT was shown to result in the transcriptional up-regulation of ATP-binding cassette, subfamily C, member 3 (ABCC3), a member of the ABC transporter superfamily, which has a recognized role in multidrug resistance. Buffering of cytosolic free calcium inhibited EGF-mediated ABCC3 increases, indicating a calcium-dependent mode of regulation. Silencing of TRPM7 (an ion channel involved in EMT associated vimentin induction) did not inhibit ABCC3 up-regulation. Silencing of the store operated calcium entry (SOCE) pathway components ORAI1 and STIM1 also did not alter ABCC3 induction by EGF. However, the calcium permeable ion channel transient receptor potential cation channel, subfamily C, member 1 (TRPC1) appears to contribute to the regulation of both basal and EGF-induced ABCC3 mRNA. Improved understanding of the relationship between calcium signaling, EMT and the regulation of genes important in therapeutic resistance may help identify novel therapeutic targets for breast cancer. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular Docking Analysis of Ginger Active Compound on Transient Receptor Potential Cation Channel Subfamily V Member 1 (TRPV1

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Fifteen Aprila Fajrin

2018-02-01

Full Text Available Ginger had been reported to ameliorate painful diabetic neuropathy (PDN in an animal model. Gingerol and shogaol were active compounds of ginger that potentially act on transient receptor potential cation channel subfamily V member 1 (TRPV1, a key receptor in PDN. This study aims to predict the binding of gingerol and shogaol to TRPV1 using an in silico model. The ligands of the docking study were 3 chemical compounds of each gingerol and shogaol, i.e. 6-shogaol, 8-shogaol, 10-shogaol, 6-gingerol, 8 gingerol and 10-gingerol. Capsaicin, a TRPV1 agonist, was used as a native ligand. The TRPV1 structure was taken from Protein Data Bank (ID 3J9J. The docking analysis was performed using Autodock Vina. The result showed that among the ginger active compounds, 6-shogaol had the strongest binding energy (-7.10 kcal/mol to TRPV1. The 6-shogaol lacked the potential hydrogen bond to Ile265 of TRPV1 protein, which capsacin had. However, it's binding energy towards TRPV1 was not significantly different compared to capsaicin. Therefore, 6-shogaol had potential to be developed as a treatment for PDN.

Getting from A to B-exploring the activation motifs of the class B adhesion G protein-coupled receptor subfamily G member 4/GPR112

DEFF Research Database (Denmark)

Cornelia Peeters, Miriam; Mos, Iris; Lenselink, Eelke B

2016-01-01

The adhesion G protein-coupled receptors (ADGRs/class B2 G protein-coupled receptors) constitute an ancient family of G protein-coupled receptors that have recently been demonstrated to play important roles in cellular and developmental processes. Here, we describe a first insight...... into the structure-function relationship of ADGRs using the family member ADGR subfamily G member 4 (ADGRG4)/GPR112 as a model receptor. In a bioinformatics approach, we compared conserved, functional elements of the well-characterized class A and class B1 secretin-like G protein-coupled receptors with the ADGRs. We...... identified several potential equivalent motifs and subjected those to mutational analysis. The importance of the mutated residues was evaluated by examining their effect on the high constitutive activity of the N-terminally truncated ADGRG4/GPR112 in a 1-receptor-1-G protein Saccharomyces cerevisiae...

Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies.

Science.gov (United States)

Jung, Sook; Cestaro, Alessandro; Troggio, Michela; Main, Dorrie; Zheng, Ping; Cho, Ilhyung; Folta, Kevin M; Sosinski, Bryon; Abbott, Albert; Celton, Jean-Marc; Arús, Pere; Shulaev, Vladimir; Verde, Ignazio; Morgante, Michele; Rokhsar, Daniel; Velasco, Riccardo; Sargent, Daniel James

2012-04-04

Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes. Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA) algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes. Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.

Multilocus molecular phylogeny of the suckermouth armored catfishes (Siluriformes: Loricariidae) with a focus on subfamily Hypostominae.

Science.gov (United States)

Lujan, Nathan K; Armbruster, Jonathan W; Lovejoy, Nathan R; López-Fernández, Hernán

2015-01-01

The Neotropical catfish family Loricariidae is the fifth most species-rich vertebrate family on Earth, with over 800 valid species. The Hypostominae is its most species-rich, geographically widespread, and ecomorphologically diverse subfamily. Here, we provide a comprehensive molecular phylogenetic reappraisal of genus-level relationships in the Hypostominae based on our sequencing and analysis of two mitochondrial and three nuclear loci (4293bp total). Our most striking large-scale systematic discovery was that the tribe Hypostomini, which has traditionally been recognized as sister to tribe Ancistrini based on morphological data, was nested within Ancistrini. This required recognition of seven additional tribe-level clades: the Chaetostoma Clade, the Pseudancistrus Clade, the Lithoxus Clade, the 'Pseudancistrus' Clade, the Acanthicus Clade, the Hemiancistrus Clade, and the Peckoltia Clade. Results of our analysis, which included type- and non-type species for every valid genus in Hypostominae, support the reevaluation and restriction of several historically problematic genera, including Baryancistrus, Cordylancistrus, Hemiancistrus, and Peckoltia. Much of the deep lineage diversity in Hypostominae is restricted to Guiana Shield and northern Andean drainages, with three tribe-level clades still largely restricted to the Guiana Shield. Of the six geographically widespread clades, a paraphyletic assemblage of three contain lineages restricted to drainages west of the Andes Mountains, suggesting that early diversification of the Hypostominae predated the late Miocene surge in Andean uplift. Our results also highlight examples of trophic ecological diversification and convergence in the Loricariidae, including support for three independent origins of highly similar and globally unique morphological specializations for eating wood. Copyright © 2014 Elsevier Inc. All rights reserved.

Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA

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Arafat Rahman Oany

2017-01-01

Full Text Available Shigellosis, a bacillary dysentery, is closely associated with diarrhoea in human and causes infection of 165 million people worldwide per year. Casein-degrading serine protease autotransporter of enterobacteriaceae (SPATE subfamily protein SigA, an outer membrane protein, exerts both cytopathic and enterotoxic effects especially cytopathic to human epithelial cell type-2 (HEp-2 and is shown to be highly immunogenic. In the present study, we have tried to impose the vaccinomics approach for designing a common peptide vaccine candidate against the immunogenic SigA of Shigella spp. At first, 44 SigA proteins from different variants of S. flexneri, S. dysenteriae, S. boydii, and S. sonnei were assessed to find the most antigenic protein. We retrieved 12 peptides based on the highest score for human leukocyte antigen (HLA supertypes analysed by NetCTL. Initially, these peptides were assessed for the affinity with MHC class I and class II alleles, and four potential core epitopes VTARAGLGY, FHTVTVNTL, HTTWTLTGY, and IELAGTLTL were selected. From these, FHTVTVNTL and IELAGTLTL peptides were shown to have 100% conservancy. Finally, IELAGTLTL was shown to have the highest population coverage (83.86% among the whole world population. In vivo study of the proposed epitope might contribute to the development of functional and unique widespread vaccine, which might be an operative alleyway to thwart dysentery from the world.

Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies

Directory of Open Access Journals (Sweden)

Jung Sook

2012-04-01

Full Text Available Abstract Background Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes. Results Our analysis using the whole genome sequences of peach, apple and strawberry identified 1399 orthologous regions between the three genomes, with a mean length of around 100 kb. Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera. However, the distribution of contiguous ancestral regions, identified using the multiple genome rearrangements and ancestors (MGRA algorithm, suggested that the Fragaria genome went through a greater number of small scale rearrangements compared to the other genomes since they diverged from a common ancestor. Using the contiguous ancestral regions, we reconstructed a hypothetical ancestral genome for the Rosaceae 7 composed of nine chromosomes and propose the evolutionary steps from the ancestral genome to the extant Fragaria, Prunus and Malus genomes. Conclusion Our analysis shows that different modes of evolution may have played major roles in different subfamilies of Rosaceae. The hypothetical ancestral genome of Rosaceae and the evolutionary steps that lead to three different lineages of Rosaceae will facilitate our understanding of plant genome evolution as well as have a practical impact on knowledge transfer among member species of Rosaceae.

Morphological "primary homology" and expression of AG-subfamily MADS-box genes in pines, podocarps, and yews.

Science.gov (United States)

Englund, Marie; Carlsbecker, Annelie; Engström, Peter; Vergara-Silva, Francisco

2011-01-01

The morphological variation among reproductive organs of extant gymnosperms is remarkable, especially among conifers. Several hypotheses concerning morphological homology between various conifer reproductive organs have been put forward, in particular in relation to the pine ovuliferous scale. Here, we use the expression patterns of orthologs of the ABC-model MADS-box gene AGAMOUS (AG) for testing morphological homology hypotheses related to organs of the conifer female cone. To this end, we first developed a tailored 3'RACE procedure that allows reliable amplification of partial sequences highly similar to gymnosperm-derived members of the AG-subfamily of MADS-box genes. Expression patterns of two novel conifer AG orthologs cloned with this procedure-namely PodAG and TgAG, obtained from the podocarp Podocarpus reichei and the yew Taxus globosa, respectively-are then further characterized in the morphologically divergent female cones of these species. The expression patterns of PodAG and TgAG are compared with those of DAL2, a previously discovered Picea abies (Pinaceae) AG ortholog. By treating the expression patterns of DAL2, PodAG, and TgAG as character states mapped onto currently accepted cladogram topologies, we suggest that the epimatium-that is, the podocarp female cone organ previously postulated as a "modified" ovuliferous scale-and the canonical Pinaceae ovuliferous scale can be legitimally conceptualized as "primary homologs." Character state mapping for TgAG suggests in turn that the aril of Taxaceae should be considered as a different type of organ. This work demonstrates how the interaction between developmental-genetic data and formal cladistic theory could fruitfully contribute to gymnosperm systematics. © 2011 Wiley Periodicals, Inc.

A novel fractal approach for predicting G-protein-coupled receptors and their subfamilies with support vector machines.

Science.gov (United States)

Nie, Guoping; Li, Yong; Wang, Feichi; Wang, Siwen; Hu, Xuehai

2015-01-01

G-protein-coupled receptors (GPCRs) are seven membrane-spanning proteins and regulate many important physiological processes, such as vision, neurotransmission, immune response and so on. GPCRs-related pathways are the targets of a large number of marketed drugs. Therefore, the design of a reliable computational model for predicting GPCRs from amino acid sequence has long been a significant biomedical problem. Chaos game representation (CGR) reveals the fractal patterns hidden in protein sequences, and then fractal dimension (FD) is an important feature of these highly irregular geometries with concise mathematical expression. Here, in order to extract important features from GPCR protein sequences, CGR algorithm, fractal dimension and amino acid composition (AAC) are employed to formulate the numerical features of protein samples. Four groups of features are considered, and each group is evaluated by support vector machine (SVM) and 10-fold cross-validation test. To test the performance of the present method, a new non-redundant dataset was built based on latest GPCRDB database. Comparing the results of numerical experiments, the group of combined features with AAC and FD gets the best result, the accuracy is 99.22% and Matthew's correlation coefficient (MCC) is 0.9845 for identifying GPCRs from non-GPCRs. Moreover, if it is classified as a GPCR, it will be further put into the second level, which will classify a GPCR into one of the five main subfamilies. At this level, the group of combined features with AAC and FD also gets best accuracy 85.73%. Finally, the proposed predictor is also compared with existing methods and shows better performances.

Evolution of the miR5200-FLOWERING LOCUS T flowering time regulon in the temperate grass subfamily Pooideae.

Science.gov (United States)

McKeown, Meghan; Schubert, Marian; Preston, Jill C; Fjellheim, Siri

2017-09-01

Flowering time is a carefully regulated trait controlled primarily through the action of the central genetic regulator, FLOWERING LOCUS T (FT). Recently it was demonstrated that a microRNA, miR5200, targets the end of the second exon of FT under short-day photoperiods in the grass subfamily Pooideae, thus preventing FT transcripts from reaching threshold levels under non-inductive conditions. Pooideae are an interesting group in that they rapidly diversified from the tropics into the northern temperate region during a major global cooling event spanning the Eocene-Oligocene transition. We hypothesize that miR5200 photoperiod-sensitive regulation of Pooideae flowering time networks assisted their transition into northern seasonal environments. Here, we test predictions derived from this hypothesis that miR5200, originally found in bread wheat and later identified in Brachypodium distachyon, (1) was present in the genome of the Pooideae common ancestor, (2) is transcriptionally regulated by photoperiod, and (3) is negatively correlated with FT transcript abundance, indicative of miR5200 regulating FT. Our results demonstrate that miR5200 did evolve at or around the base of Pooideae, but only acquired photoperiod-regulated transcription within the Brachypodium lineage. Based on expression profiles and previous data, we posit that the progenitor of miR5200 was co-regulated with FT by an unknown mechanism. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice.

Science.gov (United States)

Chen, Guoxiong; Komatsuda, Takao; Ma, Jian Feng; Nawrath, Christiane; Pourkheirandish, Mohammad; Tagiri, Akemi; Hu, Yin-Gang; Sameri, Mohammad; Li, Xinrong; Zhao, Xin; Liu, Yubing; Li, Chao; Ma, Xiaoying; Wang, Aidong; Nair, Sudha; Wang, Ning; Miyao, Akio; Sakuma, Shun; Yamaji, Naoki; Zheng, Xiuting; Nevo, Eviatar

2011-07-26

Land plants have developed a cuticle preventing uncontrolled water loss. Here we report that an ATP-binding cassette (ABC) subfamily G (ABCG) full transporter is required for leaf water conservation in both wild barley and rice. A spontaneous mutation, eibi1.b, in wild barley has a low capacity to retain leaf water, a phenotype associated with reduced cutin deposition and a thin cuticle. Map-based cloning revealed that Eibi1 encodes an HvABCG31 full transporter. The gene was highly expressed in the elongation zone of a growing leaf (the site of cutin synthesis), and its gene product also was localized in developing, but not in mature tissue. A de novo wild barley mutant named "eibi1.c," along with two transposon insertion lines of rice mutated in the ortholog of HvABCG31 also were unable to restrict water loss from detached leaves. HvABCG31 is hypothesized to function as a transporter involved in cutin formation. Homologs of HvABCG31 were found in green algae, moss, and lycopods, indicating that this full transporter is highly conserved in the evolution of land plants.

Convergent, Parallel and Correlated Evolution of Trophic Morphologies in the Subfamily Schizothoracinae from the Qinghai-Tibetan Plateau

Science.gov (United States)

Qi, Delin; Chao, Yan; Guo, Songchang; Zhao, Lanying; Li, Taiping; Wei, Fulei; Zhao, Xinquan

2012-01-01

Schizothoracine fishes distributed in the water system of the Qinghai-Tibetan plateau (QTP) and adjacent areas are characterized by being highly adaptive to the cold and hypoxic environment of the plateau, as well as by a high degree of diversity in trophic morphology due to resource polymorphisms. Although convergent and parallel evolution are prevalent in the organisms of the QTP, it remains unknown whether similar evolutionary patterns have occurred in the schizothoracine fishes. Here, we constructed for the first time a tentative molecular phylogeny of the schizothoracine fishes based on the complete sequences of the cytochrome b gene. We employed this molecular phylogenetic framework to examine the evolution of trophic morphologies. We used Pagel's maximum likelihood method to estimate the evolutionary associations of trophic morphologies and food resource use. Our results showed that the molecular and published morphological phylogenies of Schizothoracinae are partially incongruent with respect to some intergeneric relationships. The phylogenetic results revealed that four character states of five trophic morphologies and of food resource use evolved at least twice during the diversification of the subfamily. State transitions are the result of evolutionary patterns including either convergence or parallelism or both. Furthermore, our analyses indicate that some characters of trophic morphologies in the Schizothoracinae have undergone correlated evolution, which are somewhat correlated with different food resource uses. Collectively, our results reveal new examples of convergent and parallel evolution in the organisms of the QTP. The adaptation to different trophic niches through the modification of trophic morphologies and feeding behaviour as found in the schizothoracine fishes may account for the formation and maintenance of the high degree of diversity and radiations in fish communities endemic to QTP. PMID:22470515

Transient receptor potential melastatin subfamily member 2 cation channel regulates detrimental immune cell invasion in ischemic stroke.

Science.gov (United States)

Gelderblom, Mathias; Melzer, Nico; Schattling, Benjamin; Göb, Eva; Hicking, Gordon; Arunachalam, Priyadharshini; Bittner, Stefan; Ufer, Friederike; Herrmann, Alexander M; Bernreuther, Christian; Glatzel, Markus; Gerloff, Christian; Kleinschnitz, Christoph; Meuth, Sven G; Friese, Manuel A; Magnus, Tim

2014-11-01

Brain injury during stroke results in oxidative stress and the release of factors that include extracellular Ca(2+), hydrogen peroxide, adenosine diphosphate ribose, and nicotinic acid adenine dinucleotide phosphate. These alterations of the extracellular milieu change the activity of transient receptor potential melastatin subfamily member 2 (TRPM2), a nonselective cation channel expressed in the central nervous system and the immune system. Our goal was to evaluate the contribution of TRPM2 to the tissue damage after stroke. In accordance with current quality guidelines, we independently characterized Trpm2 in a murine ischemic stroke model in 2 different laboratories. Gene deficiency of Trpm2 resulted in significantly improved neurological outcome and decreased infarct size. Besides an already known moderate neuroprotective effect of Trpm2 deficiency in vitro, ischemic brain invasion by neutrophils and macrophages was particularly reduced in Trpm2-deficient mice. Bone marrow chimeric mice revealed that Trpm2 deficiency in the peripheral immune system is responsible for the protective phenotype. Furthermore, experiments with mixed bone marrow chimeras demonstrated that Trpm2 is essential for the migration of neutrophils and, to a lesser extent, also of macrophages into ischemic hemispheres. Notably, the pharmacological TRPM2 inhibitor, N-(p-amylcinnamoyl)anthranilic acid, was equally protective in the stroke model. Although a neuroprotective effect of TRPM2 in vitro is well known, we can show for the first time that the detrimental role of TRPM2 in stroke primarily depends on its role in activating peripheral immune cells. Targeting TRPM2 systemically represents a promising therapeutic approach for ischemic stroke. © 2014 American Heart Association, Inc.

A new genus and species of entocytherid ostracod (Ostracoda: Entocytheridae) from the John Day River Basin of Oregon, U.S.A., with a key to genera of the subfamily Entocytherinae.

Science.gov (United States)

Weaver, Patricia G; Williams, Bronwyn W

2017-06-07

Targeted sampling efforts by the authors for the signal crayfish, Pacifastacus leniusculus, from its native range in the John Day River Basin, Oregon, U.S.A. yielded entocytherid ostracods with a male copulatory complex so clearly different from other entocytherines that a new genus, Aurumcythere gen. nov. is proposed to receive them. This newly proposed, apparently nonsclerotized, genus with hook and spur-like prominences of the posteroventral end of the peniferum is the first new genus of the subfamily Entocytherinae named since Hobbs & Peters described Aphelocythere (= Waltoncythere) in 1977. Aurumcythere gen. nov. represents only the second genus of entocytherid known from the Pacific Northwest. Lack of sclerotization in Aurumcythere gen. nov. provides new insight into poorly understood mating behaviors of entocytherid ostracods.

Transient receptor potential cation channel, subfamily C, member 5 (TRPC5) is a cold-transducer in the peripheral nervous system.

Science.gov (United States)

Zimmermann, Katharina; Lennerz, Jochen K; Hein, Alexander; Link, Andrea S; Kaczmarek, J Stefan; Delling, Markus; Uysal, Serdar; Pfeifer, John D; Riccio, Antonio; Clapham, David E

2011-11-01

Detection and adaptation to cold temperature is crucial to survival. Cold sensing in the innocuous range of cold (>10-15 °C) in the mammalian peripheral nervous system is thought to rely primarily on transient receptor potential (TRP) ion channels, most notably the menthol receptor, TRPM8. Here we report that TRP cation channel, subfamily C member 5 (TRPC5), but not TRPC1/TRPC5 heteromeric channels, are highly cold sensitive in the temperature range 37-25 °C. We found that TRPC5 is present in mouse and human sensory neurons of dorsal root ganglia, a substantial number of peripheral nerves including intraepithelial endings, and in the dorsal lamina of the spinal cord that receives sensory input from the skin, consistent with a potential TRPC5 function as an innocuous cold transducer in nociceptive and thermosensory nerve endings. Although deletion of TRPC5 in 129S1/SvImJ mice resulted in no temperature-sensitive behavioral changes, TRPM8 and/or other menthol-sensitive channels appear to underpin a much larger component of noxious cold sensing after TRPC5 deletion and a shift in mechanosensitive C-fiber subtypes. These findings demonstrate that highly cold-sensitive TRPC5 channels are a molecular component for detection and regional adaptation to cold temperatures in the peripheral nervous system that is distinct from noxious cold sensing.

Genome wide identification and expression analysis of Homeodomain leucine zipper subfamily IV (HDZ IV gene family from Musa accuminata

Directory of Open Access Journals (Sweden)

Ashutosh ePandey

2016-02-01

Full Text Available The homedodomain zipper family (HD-ZIP of transcription factors is present only in plants and plays important role in the regulation of plant-specific processes. The subfamily IV of HDZ transcription factors (HD-ZIP IV has primarily been implicated in the regulation of epidermal structure development. Though this gene family is present in all lineages of land plants, members of this gene family have not been identified in banana, which is one of the major staple fruit crops. In the present work, we identified 21 HDZIV genes in banana by the computational analysis of banana genome resource. Our analysis suggested that these genes putatively encode proteins having all the characteristic domains of HDZIV transcription factors. The phylogenetic analysis of the banana HDZIV family genes further confirmed that after separation from a common ancestor, the banana and poales lineages might have followed distinct evolutionary paths. Further, we conclude that segmental duplication played a major role in the evolution of banana HDZIV genes. All the identified banana HDZIV genes expresses in different banana tissue, however at varying levels. The transcript levels of some of the banana HDZIV genes were also detected in banana fruit pulp, suggesting their putative role in fruit attributes. A large number of genes of this family showed modulated expression under drought and salinity stress. Taken together, the present work lays a foundation for elucidation of functional aspects of the banana HDZIV genes and for their possible use in the banana improvement programs.

Cytochrome P450 CYP3A in marsupials: cloning and characterisation of the second identified CYP3A subfamily member, isoform 3A78 from koala (Phascolarctos cinereus).

Science.gov (United States)

El-Merhibi, Adaweyah; Ngo, Suong N T; Crittenden, Tamara A; Marchant, Ceilidh L; Stupans, Ieva; McKinnon, Ross A

2011-11-01

Cytochromes P450 (CYPs) are critically important in the oxidative metabolism of a diverse array of xenobiotics and endogenous substrates. Previously, we cloned and characterised the CYP2C, CYP4A, and CYP4B gene subfamilies from marsupials and demonstrated important species-differences in both activity and tissue expression of these CYP enzymes. Recently, we isolated the Eastern grey kangaroo CYP3A70. Here we have cloned and characterised the second identified member of marsupial CYP3A gene subfamily, CYP3A78 from the koala (Phascolarctos cinereus). In addition, we have examined the gender-differences in microsomal erythromycin N-demethylation activity (a CYP3A marker) and CYP3A protein expression across test marsupial species. Significant differences in hepatic erythromycin N-demethylation activity were observed between male and female koalas, with the activity detected in female koalas being 2.5-fold higher compared to that in male koalas (p<0.01). No gender-differences were observed in tammar wallaby or Eastern grey kangaroo. Immunoblot analysis utilising anti-human CYP3A4 antibody detected immunoreactive proteins in liver microsomes from all test male and female marsupials including the koala, tammar wallaby, and Eastern grey kangaroo, with no gender-differences detected across test marsupials. A 1610 bp koala hepatic CYP3A complete cDNA, designated CYP3A78, was cloned by reverse transcription-polymerase chain reaction approaches. It displays 64% nucleotide and 57% amino acid sequence identity to the Eastern grey kangaroo CYP3A70. The CYP3A78 cDNA encodes a protein of 515 amino acids, shares approximately 68% nucleotide and 56% amino acid sequence identity to human CYP3A4, and displays high sequence similarity to other published mammalian CYP3As from human, monkey, cow, pig, dog, rat, rabbit, mouse, hamster, and guinea pig. Collectively, this study provides primary molecular data regarding koala hepatic CYP3A78 gene and enables further functional analyses of CYP

The ZNF75 zinc finger gene subfamily: Isolation and mapping of the four members in humans and great apes

Energy Technology Data Exchange (ETDEWEB)

Villa, A.; Strina, D.; Frattini, A. [Consiglio Nazionale delle Ricerche, Milan (Italy)] [and others

1996-07-15

We have previously reported the characterization of the human ZNF75 gene located on Xq26, which has only limited homology (less than 65%) to other ZF genes in the databases. Here, we describe three human zinc finger genes with 86 to 95% homology to ZNF75 at the nucleotide level, which represent all the members of the human ZNF75 subfamily. One of these, ZNF75B, is a pseudogene mapped to chromosome 12q13. The other two, ZNF75A and ZNF75C, maintain on ORF in the sequenced region, and at least the latter is expressed in the U937 cell line. They were mapped to chromosomes 16 and 11, respectively. All these genes are conserved in chimpanzees, gorillas, and orangutans. The ZNF75B homologue is a pseudogene in all three great apes, and in chimpanzee it is located on chromosome 10 (phylogenetic XII), at p13 (corresponding to the human 12q13). The chimpanzee homologue of ZNF75 is also located on the Xq26 chromosome, in the same region, as detected by in situ hybridization. As expected, nucleotide changes were clearly more abundant between human and organutan than between human and chimpanzee or gorilla homologues. Members of the same class were more similar to each other than to the other homologues within the same species. This suggests that the duplication and/or retrotranscription events occurred in a common ancestor long before great ape speciation. This, together with the existance of at least two genes in cows and horses, suggests a relatively high conservation of this gene family. 20 refs., 5 figs., 1 tab.

Comparative studies of a new subfamily of human Ste20-like kinases: homodimerization, subcellular localization, and selective activation of MKK3 and p38.

Science.gov (United States)

Yustein, Jason T; Xia, Liang; Kahlenburg, J Michelle; Robinson, Dan; Templeton, Dennis; Kung, Hsing-Jien

2003-09-18

The Sterile-20 or Ste20 family of serine/threonine kinases is a group of signaling molecules whose physiological roles within mammalian cells are just starting to be elucidated. Here, in this report we present the characterization of three human Ste20-like kinases with greater than 90% similarity within their catalytic domains that define a novel subfamily of Ste20s. Members of this kinase family include rat thousand and one (TAO1) and chicken KFC (kinase from chicken). For the lack of a consensus nomenclature in the literature, in this report, we shall call this family hKFC (for their homology to chicken KFC) and the three members hKFC-A, hKFC-B, and hKFC-C, respectively. These kinases have many similarities including an aminoterminal kinase domain, a serine-rich region, and a coiled-coil configuration within the C-terminus. All three kinases are able to activate the p38 MAP kinase pathway through the specific activation of the upstream MKK3 kinase. We also offer evidence, both theoretical and biochemical, showing that these kinases can undergo self-association. Despite these similarities, these kinases differ in tissue distribution, apparent subcellular localization, and feature structural differences largely within the carboxyl-terminal sequence.

A new member of the GM130 golgin subfamily is expressed in the optic lobe anlagen of the metamorphosing brain of Manduca sexta

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Chiou-Miin Wang

2003-12-01

Full Text Available During metamorphosis of the insect brain, the optic lobe anlagen generate the proliferation centers for the visual cortices. We show here that, in the moth Manduca sexta, an 80 kDa Golgi complex protein (Ms-golgin80 is abundantly expressed in the cytoplasm of neuroblasts and ganglion mother cells in the optic lobe anlagen and proliferation centers. The predicted amino acid sequence for Ms-golgin80 is similar to that of several members of the GM130 subfamily of Golgi-associated proteins, including rat GM130 and human golgin-95. Homologs of Ms-golgin80 from Drosophila melanogaster, Caenorhabditis elegans, and Brugia malayi were identified through homology sequence search. Sequence similarities are present in three regions: the N-terminus, an internal domain of 89 amino acids, and another domain of 89 amino acids near the C-terminus. Structural similarities further suggest that these molecules play the same cellular role as GM130. GM130 is involved in the docking and fusion of coatomer (COP I coated vesicles to the Golgi membranes; it also regulates the fragmentation and subsequent reassembly of the Golgi complex during mitosis. Abundant expression of Ms-golgin80 in neuroblasts and ganglion mother cells and its reduced expression in the neuronal progeny of these cells suggest that this protein may be involved in the maintenance of the proliferative state.

Modelling and mutational analysis of Aspergillus nidulans UreA, a member of the subfamily of urea/H+ transporters in fungi and plants

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Sanguinetti, Manuel; Amillis, Sotiris; Pantano, Sergio; Scazzocchio, Claudio; Ramón, Ana

2014-01-01

We present the first account of the structure–function relationships of a protein of the subfamily of urea/H+ membrane transporters of fungi and plants, using Aspergillus nidulans UreA as a study model. Based on the crystal structures of the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT) and of the Nucleobase-Cation-Symport-1 benzylhydantoin transporter from Microbacterium liquefaciens (Mhp1), we constructed a three-dimensional model of UreA which, combined with site-directed and classical random mutagenesis, led to the identification of amino acids important for UreA function. Our approach allowed us to suggest roles for these residues in the binding, recognition and translocation of urea, and in the sorting of UreA to the membrane. Residues W82, Y106, A110, T133, N275, D286, Y388, Y437 and S446, located in transmembrane helixes 2, 3, 7 and 11, were found to be involved in the binding, recognition and/or translocation of urea and the sorting of UreA to the membrane. Y106, A110, T133 and Y437 seem to play a role in substrate selectivity, while S446 is necessary for proper sorting of UreA to the membrane. Other amino acids identified by random classical mutagenesis (G99, R141, A163, G168 and P639) may be important for the basic transporter's structure, its proper folding or its correct traffic to the membrane. PMID:24966243

A REVISION OF THE PLIOCENE NATICIDS OF NORTHERN AND CENTRAL ITALY. II. THE SUBFAMILY NATICINAE: ADDITIONS TO COCHLIS, TANEA AND TECTONATICA

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LUCA PEDRIALI

2008-03-01

Full Text Available The present paper is the second in a series devoted to the revision of the Pliocene naticids of Northern and Central Italy. It concludes the section covering the calcareous operculum-bearing Naticinae and expands to 18 the total number of species and subspecies of this subfamily recovered so far from the Pliocene deposits of Italy. Of the six taxa considered in this study, two (epigloafuniculata and fredianii fully match the characters of the genus Cochlis Röding, 1798, one (koeneni is assigned to the genus Tanea Marwick, 1931, the rest (astensis, prietoi and tectula belong to the genus Tectonatica Sacco, 1890. All the six taxa considered in this paper are described and commented in the systematic account. One, Cochlis fredianii, is proposed as new. In the chapter treating the generic assignment of the studied taxa, the range of Tanea, hitherto used to allocate several Indo-Pacific species, is extended to the Mediterranean Basin as well, and the relations between Tectonatica and Cryptonatica Dall, 1892 are discussed. This study further demonstrates that the morphological characters of the teleoconch are of low significance in species recognition. In fact, should the characters be ranked, the operculum comes first and is the primary element, sufficient to distinguish each species. The protoconch and the color pattern are the second and third relevant attributes that can be used diagnostically for several taxa, but not always. The other shell features appear to be useful tools in separating species only occasionally. Some species lack distinctive shell characters and do require operculate specimens in order to be confidently 

Giant panda (Ailuropoda melanoleuca) population dynamics and bamboo (subfamily Bambusoideae) life history: a structured population approach to examining carrying capacity when the prey are semelparous

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Carter, J.; Ackleh, A.S.; Leonard, B.P.; Wang, Hongfang

1999-01-01

The giant panda, Ailuropoda melanoleuca, is a highly specialized Ursid whose diet consists almost entirely of various species of bamboo. Bamboo (Bambusoideae) is a grass subfamily whose species often exhibit a synchronous semelparity. Synchronous semelparity can create local drops in carrying capacity for the panda. We modeled the interaction of pandas and their bamboo food resources with an age structured panda population model linked to a natural history model of bamboo biomass dynamics based on literature values of bamboo biomass, and giant panda life history dynamics. This paper reports the results of our examination of the interaction between pandas and their bamboo food resource and its implications for panda conservation. In the model all panda populations were well below the carrying capacity of the habitat. The giant panda populations growth was most sensitive to changes in birth rates and removal of reproductive aged individuals. Periodic starvation that has been documented in conjunction with bamboo die-offs is probably related to the inability to move to other areas within the region where bamboo is still available. Based on the results of this model, giant panda conservation should concentrate on keeping breeding individuals in the wild, keep corridors to different bamboo species open to pandas, and to concentrate research on bamboo life history.

Role of NH2-terminal hydrophobic motif in the subcellular localization of ATP-binding cassette protein subfamily D: Common features in eukaryotic organisms

International Nuclear Information System (INIS)

Lee, Asaka; Asahina, Kota; Okamoto, Takumi; Kawaguchi, Kosuke; Kostsin, Dzmitry G.; Kashiwayama, Yoshinori; Takanashi, Kojiro; Yazaki, Kazufumi; Imanaka, Tsuneo; Morita, Masashi

2014-01-01

Highlights: • ABCD proteins classifies based on with or without NH 2 -terminal hydrophobic segment. • The ABCD proteins with the segment are targeted peroxisomes. • The ABCD proteins without the segment are targeted to the endoplasmic reticulum. • The role of the segment in organelle targeting is conserved in eukaryotic organisms. - Abstract: In mammals, four ATP-binding cassette (ABC) proteins belonging to subfamily D have been identified. ABCD1–3 possesses the NH 2 -terminal hydrophobic region and are targeted to peroxisomes, while ABCD4 lacking the region is targeted to the endoplasmic reticulum (ER). Based on hydropathy plot analysis, we found that several eukaryotes have ABCD protein homologs lacking the NH 2 -terminal hydrophobic segment (H0 motif). To investigate whether the role of the NH 2 -terminal H0 motif in subcellular localization is conserved across species, we expressed ABCD proteins from several species (metazoan, plant and fungi) in fusion with GFP in CHO cells and examined their subcellular localization. ABCD proteins possessing the NH 2 -terminal H0 motif were localized to peroxisomes, while ABCD proteins lacking this region lost this capacity. In addition, the deletion of the NH 2 -terminal H0 motif of ABCD protein resulted in their localization to the ER. These results suggest that the role of the NH 2 -terminal H0 motif in organelle targeting is widely conserved in living organisms

A família Rubiaceae na Reserva Biológica Guaribas, Paraíba, Brasil: subfamílias Antirheoideae, Cinchonoideae e Ixoroideae The family Rubiaceae in the Guaribas Biological Reserve, Paraíba State, Brazil: subfamilies Antirheoideae, Cinchonoideae and Ixoroideae

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Maria do Socorro Pereira

2004-06-01

Full Text Available Este trabalho consiste no levantamento dos representantes das subfamílias Antirheoideae, Cinchonoideae e Ixoroideae na Reserva Biológica Guaribas, Paraíba, Brasil. Foram realizadas coletas intensivas no período de outubro/2000 a outubro/2001, as quais resultaram no reconhecimento de 12 espécies, 10 gêneros e cinco tribos, distribuídos nas três subfamílias. A subfamília melhor representada foi Antirheoideae, com cinco espécies, quatro gêneros e duas tribos. Os gêneros com maior número de espécies foram Guettarda L. (2 e Tocoyena Aubl. (2. Alibertia A. Rich. ex DC., Alseis Schott, Chiococca P. Browne, Chomelia Jacq., Coutarea Aubl., Posoqueria Aubl., Sabicea Aubl. e Salzmannia DC. apresentaram uma única espécie cada. São apresentadas chaves para identificação, descrições, comentários sobre morfologia e distribuição das espécies, e ilustrações dos táxons verificados.This paper is a survey of Rubiaceae subfamilies Antirheoideae, Cinchonoideae and Ixoroideae in the Guaribas Biological Reserve, Paraíba, Brazil. Intensive collections were made from October/2000 to October/2001. Twelve species, 10 genera and five tribes were recognized. The most diverse subfamily was Antirheoideae, with five species, four genera and two tribes. The genera with the most species were Guettarda L. (2 and Tocoyena Aubl. (2. Alibertia A. Rich. ex DC., Alseis Schott, Chiococca P. Browne, Chomelia Jacq., Coutarea Aubl., Posoqueria Aubl., Sabicea Aubl., and Salzmannia DC. were represented by only one species each. Keys, descriptions, comments on morphology and species distributions, as well as illustrations of the taxa are provided.

Crystal structures of two transcriptional regulators from Bacillus cereus define the conserved structural features of a PadR subfamily.

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Guntur Fibriansah

Full Text Available PadR-like transcriptional regulators form a structurally-related family of proteins that control the expression of genes associated with detoxification, virulence and multi-drug resistance in bacteria. Only a few members of this family have been studied by genetic, biochemical and biophysical methods, and their structure/function relationships are still largely undefined. Here, we report the crystal structures of two PadR-like proteins from Bacillus cereus, which we named bcPadR1 and bcPadR2 (products of gene loci BC4206 and BCE3449 in strains ATCC 14579 and ATCC 10987, respectively. BC4206, together with its neighboring gene BC4207, was previously shown to become significantly upregulated in presence of the bacteriocin AS-48. DNA mobility shift assays reveal that bcPadR1 binds to a 250 bp intergenic region containing the putative BC4206-BC4207 promoter sequence, while in-situ expression of bcPadR1 decreases bacteriocin tolerance, together suggesting a role for bcPadR1 as repressor of BC4206-BC4207 transcription. The function of bcPadR2 (48% identical in sequence to bcPadR1 is unknown, but the location of its gene just upstream from genes encoding a putative antibiotic ABC efflux pump, suggests a role in regulating antibiotic resistance. The bcPadR proteins are structurally similar to LmrR, a PadR-like transcription regulator in Lactococcus lactis that controls expression of a multidrug ABC transporter via a mechanism of multidrug binding and induction. Together these proteins define a subfamily of conserved, relatively small PadR proteins characterized by a single C-terminal helix for dimerization. Unlike LmrR, bcPadR1 and bcPadR2 lack a central pore for ligand binding, making it unclear whether the transcriptional regulatory roles of bcPadR1 and bcPadR2 involve direct ligand recognition and induction.

AOX1-Subfamily Gene Members in Olea europaea cv. "Galega Vulgar"-Gene Characterization and Expression of Transcripts during IBA-Induced in Vitro Adventitious Rooting.

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Velada, Isabel; Grzebelus, Dariusz; Lousa, Diana; M Soares, Cláudio; Santos Macedo, Elisete; Peixe, Augusto; Arnholdt-Schmitt, Birgit; G Cardoso, Hélia

2018-02-17

Propagation of some Olea europaea L. cultivars is strongly limited due to recalcitrant behavior in adventitious root formation by semi-hardwood cuttings. One example is the cultivar "Galega vulgar". The formation of adventitious roots is considered a morphological response to stress. Alternative oxidase (AOX) is the terminal oxidase of the alternative pathway of the plant mitochondrial electron transport chain. This enzyme is well known to be induced in response to several biotic and abiotic stress situations. This work aimed to characterize the alternative oxidase 1 (AOX1)-subfamily in olive and to analyze the expression of transcripts during the indole-3-butyric acid (IBA)-induced in vitro adventitious rooting (AR) process. OeAOX1a (acc. no. MF410318) and OeAOX1d (acc. no. MF410319) were identified, as well as different transcript variants for both genes which resulted from alternative polyadenylation events. A correlation between transcript accumulation of both OeAOX1a and OeAOX1d transcripts and the three distinct phases (induction, initiation, and expression) of the AR process in olive was observed. Olive AOX1 genes seem to be associated with the induction and development of adventitious roots in IBA-treated explants. A better understanding of the molecular mechanisms underlying the stimulus needed for the induction of adventitious roots may help to develop more targeted and effective rooting induction protocols in order to improve the rooting ability of difficult-to-root cultivars.

Intragastric Dai-Kenchu-To, a Japanese herbal medicine, stimulates colonic motility via transient receptor potential cation channel subfamily V member 1 in dogs.

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Kikuchi, Daisuke; Shibata, Chikashi; Imoto, Hirofumi; Naitoh, Takeshi; Miura, Koh; Unno, Michiaki

2013-08-01

Japanese herbal medicine, also known as Kampo, is used for various diseases in Japan. One of those medicines, Dai-Kenchu-To (DKT), is considered clinically effective for adhesive bowel obstruction and chronic constipation. Although scientific evidence of DKT to improve adhesive bowel obstruction was shown in several previous reports, mechanism of DKT to improve constipation remains unknown. Our aim was to study the effect of intragastric DKT on colonic motility and defecation, and the involvement of various receptors in DKT-induced colonic contractions. Five beagle dogs were instructed with serosal strain-gauge force transducers to measure circular muscle activity at the proximal, middle, and distal colon. Dogs are suitable for a present study to administer the drugs repeatedly to the same individual and look at its effect on colonic motility. We studied the effects of DKT (2.5 or 5 g) administered into the stomach on colonic motility. Muscarinic receptor antagonist atropine, nicotinic receptor antagonist hexamthonium, or 5-hydroxytryptamine-3 receptor antagonist ondansetron was injected intravenously 10 min before DKT administration. Capsazepine, an antagonist to transient receptor potential cation channel subfamily V member 1 (TRPV1), was administered into the stomach 5 min before DKT administration. Intragastric DKT (2.5 or 5 g) induced colonic contractions within 10 min after administration but did not induce defecation. Pretreatment with atropine, hexamthonium, ondansetron, or capsazepine inhibited DKT-induced colonic contractions. These results indicate that orally administered DKT stimulates colonic motility via TRPV1, muscarinic, nicotinic, and 5-hydroxytryptamine-3 receptors, thereby providing scientific support for the efficacy of oral DKT in chronic constipation.

Over-expression in Escherichia coli, purification and reconstitution in liposomes of the third member of the OCTN sub-family: The mouse carnitine transporter OCTN3

International Nuclear Information System (INIS)

Scalise, Mariafrancesca; Galluccio, Michele; Pochini, Lorena; Indiveri, Cesare

2012-01-01

Highlights: ► mOCTN3 transport protein has been cloned in pET-21a(+) and over-expressed in Escherichia coli. ► The expressed mOCTN3 has been purified to homogeneity by Ni-chelating chromatography. ► The protein solubilised in Triton X-100 has been reconstituted in liposomes. ► Recombinant mOCTN3 catalyses transport of carnitine by a uniport mode. -- Abstract: pET-21a(+)-mOCTN3-6His was constructed and used for over-expression in Escherichia coli Rosetta(DE3)pLysS. After IPTG induction a protein with apparent molecular mass of 53 kDa was collected in the insoluble fraction of the cell lysate and purified by Ni 2+ -chelating chromatography with a yield of 2 mg/l of cell culture. The over-expressed protein was identified with mOCTN3 by anti-His antibody and reconstitution in liposomes. mOCTN3 required peculiar conditions for optimal expression and reconstitution in liposomes. The protein catalyzed a time dependent [ 3 H]carnitine uptake which was stimulated by intraliposomal ATP and nearly independent of the pH. The K m for carnitine was 36 μM. [ 3 H]carnitine transport was inhibited by carnitine analogues and some Cys and NH 2 reagents. This paper represents the first outcome in over-expressing, in active form, the third member of the OCTN sub-family, mOCTN3, in E. coli.

Selective ATP-Binding Cassette Subfamily C Gene Expression and Proinflammatory Mediators Released by BEAS-2B after PM2.5, Budesonide, and Cotreated Exposures

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Jarline Encarnación-Medina

2017-01-01

Full Text Available ATP-binding cassette subfamily C (ABCC genes code for phase III metabolism proteins that translocate xenobiotic (e.g., particulate matter 2.5 (PM2.5 and drug metabolites outside the cells. IL-6 secretion is related with the activation of the ABCC transporters. This study assesses ABCC1–4 gene expression changes and proinflammatory cytokine (IL-6, IL-8 release in human bronchial epithelial cells (BEAS-2B exposed to PM2.5 organic extract, budesonide (BUD, used to control inflammation in asthmatic patients, and a cotreatment (Co-T: PM2.5 and BUD. A real-time PCR assay shows that ABCC1 was upregulated in BEAS-2B exposed after 6 and 7 hr to PM2.5 extract or BUD but downregulated after 6 hr of the Co-T. ABCC3 was downregulated after 6 hr of BUD and upregulated after 6 hr of the Co-T exposures. ABCC4 was upregulated after 5 hr of PM2.5 extract, BUD, and the Co-T exposures. The cytokine assay revealed an increase in IL-6 release by BEAS-2B exposed after 5 hr to PM2.5 extract, BUD, and the Co-T. At 7 hr, the Co-T decreases IL-6 release and IL-8 at 6 hr. In conclusion, the cotreatment showed an opposite effect on exposed BEAS-2B as compared with BUD. The results suggest an interference of the BUD therapeutic potential by PM2.5.

Elephant Endotheliotropic Herpesviruses EEHV1A, EEHV1B, and EEHV2 from Cases of Hemorrhagic Disease Are Highly Diverged from Other Mammalian Herpesviruses and May Form a New Subfamily

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Richman, Laura K.; Zong, Jian-Chao; Latimer, Erin M.; Lock, Justin; Fleischer, Robert C.; Heaggans, Sarah Y.

2014-01-01

ABSTRACT A family of novel endotheliotropic herpesviruses (EEHVs) assigned to the genus Proboscivirus have been identified as the cause of fatal hemorrhagic disease in 70 young Asian elephants worldwide. Although EEHV cannot be grown in cell culture, we have determined a total of 378 kb of viral genomic DNA sequence directly from clinical tissue samples from six lethal cases and two survivors. Overall, the data obtained encompass 57 genes, including orthologues of 32 core genes common to all herpesviruses, 14 genes found in some other herpesviruses, plus 10 novel genes, including a single large putative transcriptional regulatory protein (ORF-L). On the basis of differences in gene content and organization plus phylogenetic analyses of conserved core proteins that have just 20% to 50% or less identity to orthologues in other herpesviruses, we propose that EEHV1A, EEHV1B, and EEHV2 could be considered a new Deltaherpesvirinae subfamily of mammalian herpesviruses that evolved as an intermediate branch between the Betaherpesvirinae and Gammaherpesvirinae. Unlike cytomegaloviruses, EEHV genomes encode ribonucleotide kinase B subunit (RRB), thymidine kinase (TK), and UL9-like origin binding protein (OBP) proteins and have an alphaherpesvirus-like dyad symmetry Ori-Lyt domain. They also differ from all known betaherpesviruses by having a 40-kb large-scale inversion of core gene blocks I, II, and III. EEHV1 and EEHV2 DNA differ uniformly by more than 25%, but EEHV1 clusters into two major subgroups designated EEHV1A and EEHV1B with ancient partially chimeric features. Whereas large segments are nearly identical, three nonadjacent loci totaling 15 kb diverge by between 21 and 37%. One strain of EEHV1B analyzed is interpreted to be a modern partial recombinant with EEHV1A. IMPORTANCE Asian elephants are an endangered species whose survival is under extreme pressure in wild range countries and whose captive breeding populations in zoos are not self-sustaining. In 1999, a

AOX1-Subfamily Gene Members in Olea europaea cv. “Galega Vulgar”—Gene Characterization and Expression of Transcripts during IBA-Induced in Vitro Adventitious Rooting

Science.gov (United States)

Lousa, Diana; M. Soares, Cláudio; Santos Macedo, Elisete; Arnholdt-Schmitt, Birgit

2018-01-01

Propagation of some Olea europaea L. cultivars is strongly limited due to recalcitrant behavior in adventitious root formation by semi-hardwood cuttings. One example is the cultivar ”Galega vulgar”. The formation of adventitious roots is considered a morphological response to stress. Alternative oxidase (AOX) is the terminal oxidase of the alternative pathway of the plant mitochondrial electron transport chain. This enzyme is well known to be induced in response to several biotic and abiotic stress situations. This work aimed to characterize the alternative oxidase 1 (AOX1)-subfamily in olive and to analyze the expression of transcripts during the indole-3-butyric acid (IBA)-induced in vitro adventitious rooting (AR) process. OeAOX1a (acc. no. MF410318) and OeAOX1d (acc. no. MF410319) were identified, as well as different transcript variants for both genes which resulted from alternative polyadenylation events. A correlation between transcript accumulation of both OeAOX1a and OeAOX1d transcripts and the three distinct phases (induction, initiation, and expression) of the AR process in olive was observed. Olive AOX1 genes seem to be associated with the induction and development of adventitious roots in IBA-treated explants. A better understanding of the molecular mechanisms underlying the stimulus needed for the induction of adventitious roots may help to develop more targeted and effective rooting induction protocols in order to improve the rooting ability of difficult-to-root cultivars. PMID:29462998

Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases.

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Shen, Yao-Qing; Lang, B Franz; Burger, Gertraud

2009-09-01

Acyl-CoA dehydrogenases (ACADs), which are key enzymes in fatty acid and amino acid catabolism, form a large, pan-taxonomic protein family with at least 13 distinct subfamilies. Yet most reported ACAD members have no subfamily assigned, and little is known about the taxonomic distribution and evolution of the subfamilies. In completely sequenced genomes from approximately 210 species (eukaryotes, bacteria and archaea), we detect ACAD subfamilies by rigorous ortholog identification combining sequence similarity search with phylogeny. We then construct taxonomic subfamily-distribution profiles and build phylogenetic trees with orthologous proteins. Subfamily profiles provide unparalleled insight into the organisms' energy sources based on genome sequence alone and further predict enzyme substrate specificity, thus generating explicit working hypotheses for targeted biochemical experimentation. Eukaryotic ACAD subfamilies are traditionally considered as mitochondrial proteins, but we found evidence that in fungi one subfamily is located in peroxisomes and participates in a distinct beta-oxidation pathway. Finally, we discern horizontal transfer, duplication, loss and secondary acquisition of ACAD genes during evolution of this family. Through these unorthodox expansion strategies, the ACAD family is proficient in utilizing a large range of fatty acids and amino acids-strategies that could have shaped the evolutionary history of many other ancient protein families.

Unexpected complexity of the Aquaporin gene family in the moss Physcomitrella patens

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Johanson Urban

2008-04-01

Full Text Available Abstract Background Aquaporins, also called major intrinsic proteins (MIPs, constitute an ancient superfamily of channel proteins that facilitate the transport of water and small solutes across cell membranes. MIPs are found in almost all living organisms and are particularly abundant in plants where they form a divergent group of proteins able to transport a wide selection of substrates. Results Analyses of the whole genome of Physcomitrella patens resulted in the identification of 23 MIPs, belonging to seven different subfamilies, of which only five have been previously described. Of the newly discovered subfamilies one was only identified in P. patens (Hybrid Intrinsic Protein, HIP whereas the other was found to be present in a wide variety of dicotyledonous plants and forms a major previously unrecognized MIP subfamily (X Intrinsic Proteins, XIPs. Surprisingly also some specific groups within subfamilies present in Arabidopsis thaliana and Zea mays could be identified in P. patens. Conclusion Our results suggest an early diversification of MIPs resulting in a large number of subfamilies already in primitive terrestrial plants. During the evolution of higher plants some of these subfamilies were subsequently lost while the remaining subfamilies expanded and in some cases diversified, resulting in the formation of more specialized groups within these subfamilies.

FAMILY PSYCHODIDAE.

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Bejarano, Eduar Elías; Estrada, Luis Gregorio

2016-06-14

A catalogue is presented of the species of haematophagous and non-haematophagous psychodids recorded in Colombia. The list comprises 199 species distributed among five subfamilies and 16 genera, as follows: Subfamily Bruchomyiinae, genus Nemopalpus Macquart, 1838 (4 species); subfamily Phlebotominae, genera Brumptomyia França & Parrot, 1921 (8 species), Lutzomyia França, 1924 (153 species) and Warileya Hertig, 1948 (2 species); subfamily Psychodinae, genera Arisemus Satchell, 1955 (3 species), Australopericoma Vaillant, 1975 (1 species), Balbagathis Quate, 1996 (1 species), Clogmia Enderlein, 1937 (1 species), Didicrum Enderlein, 1937 (1 species), Feuerborniella Vaillant, 1971 (1 species), Lepidiella Enderlein, 1937 (1 species), Maruina Müller, 1895 (4 species), Paramormia Enderlein, 1935 (1 species), Parasetomima Duckhouse, 1968 (1 species) and Psychoda Latreille, 1796 (7 species); subfamily Sycoracinae, genus Sycorax Haliday, 1839 (5 species); and subfamily Trichomyiinae, genus Trichomyia Haliday, 1839 (5 species).

Sex difference in induction of hepatic CYP2B and CYP3A subfamily enzymes by nicardipine and nifedipine in rats

International Nuclear Information System (INIS)

Konno, Yoshihiro; Sekimoto, Masashi; Nemoto, Kiyomitsu; Degawa, Masakuni

2004-01-01

Male and female of F344 rats were treated per os with nicardipine (Nic) and nifedipine (Nif), and changes in the levels of mRNA and protein of hepatic cytochrome P450 (P450) enzymes, CYP2B1, CYP2B2, CYP3A1, CYP3A2, CYP3A9, and CYP3A18 were examined. Furthermore, hepatic microsomal activities for pentoxyresorufin O-dealkylation (PROD) and nifedipine oxidation, which are mainly mediated by CYP2B and CYP3A subfamily enzymes, respectively, were measured. Analyses of RT-PCR and Western blotting revealed that Nic and Nif induced predominantly CYP3A and CYP2B enzymes, respectively. As for the gene activation of CYP2B enzymes, especially CYP2B1, Nif showed high capacity in both sexes of rats, whereas Nic did a definite capacity in the males but little in the females. Gene activations of CYP3A1, CYP3A2, and CYP3A18 by Nic occurred in both sexes of rats, although that of CYP3A9 did only in the male rats. Although gene activations of CYP3A1 and CYP3A2 by Nif were observed in both sexes of rats, a slight activation of the CYP3A9 gene occurred only in female rats, and the CYP3A18 gene activation, in neither male nor female rats. Thus, changes in levels of the mRNA or protein of CYP2B and CYP3A enzymes, especially CYP2B1 and CYP3A2, were closely correlated with those in hepatic PROD and nifedipine oxidation activities, respectively. The present findings demonstrate for the first time the sex difference in the Nic- and Nif-mediated induction of hepatic P450 enzymes in rats and further indicate that Nic and Nif show different specificities and sex dependencies in the induction of hepatic P450 enzymes

Potential role of melastatin-related transient receptor potential cation channel subfamily M gene expression in the pathogenesis of urinary bladder cancer.

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Ceylan, Gülay Güleç; Önalan, Ebru Etem; Kuloğlu, Tuncay; Aydoğ, Gülten; Keleş, İbrahim; Tonyali, Şenol; Ceylan, Cavit

2016-12-01

Urinary bladder cancer is one of the most common malignancies of the urinary tract. Ion channels and calcium homeostasis are involved in almost all basic cellular mechanisms. The transient receptor potential cation channel subfamily M (TRPM) takes its name from the melastatin protein, which is classified as potential tumor suppressor. To the best of our knowledge, there have been no previous studies in the literature investigating the role of these ion channels in bladder cancer. The present study aimed to determine whether bladder cancer is associated with mRNA expression levels of TRPM ion channel genes, and whether there is the potential to conduct further studies to establish novel treatment modalities. The present study included a total of 47 subjects, of whom 40 were bladder cancer patients and 7 were controls. Following the histopathological evaluation for bladder carcinoma, the mRNA and protein expression of TRPM were examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry in tumor and normal tissues, in order to determine whether there is a difference in the expression of these channels in tumor and normal tissues. Immunoreactivity for TRPM2, TRPM4, TRPM7 and TRPM8 was observed in epithelial bladder cells in the two groups. RT-qPCR revealed a significant increase in TRPM7 expression in bladder cancer tissue compared to the controls (healthy bladder tissue), whereas no differences in TRPM2 or TRPM4 expression levels were observed. There were significant reductions in the expression levels of TRPM5 and TRPM8 in bladder cancer tissues. In the present study, the effects of TRP ion channels on the formation of bladder cancer was investigated. This study is instructive for TRPM2, TRPM4, TRPM5, TRPM7 and TRPM8 and their therapeutic role in bladder cancer. The results support the fact that these gens can be novel targets and can also be tested for during the treatment of bladder cancer.

Over-expression in Escherichia coli, purification and reconstitution in liposomes of the third member of the OCTN sub-family: The mouse carnitine transporter OCTN3

Energy Technology Data Exchange (ETDEWEB)

Scalise, Mariafrancesca; Galluccio, Michele; Pochini, Lorena [Department of Cell Biology, University of Calabria, Via P. Bucci 4c, 87036 Arcavacata di Rende (Italy); Indiveri, Cesare, E-mail: indiveri@unical.it [Department of Cell Biology, University of Calabria, Via P. Bucci 4c, 87036 Arcavacata di Rende (Italy)

2012-05-25

Highlights: Black-Right-Pointing-Pointer mOCTN3 transport protein has been cloned in pET-21a(+) and over-expressed in Escherichia coli. Black-Right-Pointing-Pointer The expressed mOCTN3 has been purified to homogeneity by Ni-chelating chromatography. Black-Right-Pointing-Pointer The protein solubilised in Triton X-100 has been reconstituted in liposomes. Black-Right-Pointing-Pointer Recombinant mOCTN3 catalyses transport of carnitine by a uniport mode. -- Abstract: pET-21a(+)-mOCTN3-6His was constructed and used for over-expression in Escherichia coli Rosetta(DE3)pLysS. After IPTG induction a protein with apparent molecular mass of 53 kDa was collected in the insoluble fraction of the cell lysate and purified by Ni{sup 2+}-chelating chromatography with a yield of 2 mg/l of cell culture. The over-expressed protein was identified with mOCTN3 by anti-His antibody and reconstitution in liposomes. mOCTN3 required peculiar conditions for optimal expression and reconstitution in liposomes. The protein catalyzed a time dependent [{sup 3}H]carnitine uptake which was stimulated by intraliposomal ATP and nearly independent of the pH. The K{sub m} for carnitine was 36 {mu}M. [{sup 3}H]carnitine transport was inhibited by carnitine analogues and some Cys and NH{sub 2} reagents. This paper represents the first outcome in over-expressing, in active form, the third member of the OCTN sub-family, mOCTN3, in E. coli.

Association with the Plasma Membrane Is Sufficient for Potentiating Catalytic Activity of Regulators of G Protein Signaling (RGS) Proteins of the R7 Subfamily.

Science.gov (United States)

Muntean, Brian S; Martemyanov, Kirill A

2016-03-25

Regulators of G protein Signaling (RGS) promote deactivation of heterotrimeric G proteins thus controlling the magnitude and kinetics of responses mediated by G protein-coupled receptors (GPCR). In the nervous system, RGS7 and RGS9-2 play essential role in vision, reward processing, and movement control. Both RGS7 and RGS9-2 belong to the R7 subfamily of RGS proteins that form macromolecular complexes with R7-binding protein (R7BP). R7BP targets RGS proteins to the plasma membrane and augments their GTPase-accelerating protein (GAP) activity, ultimately accelerating deactivation of G protein signaling. However, it remains unclear if R7BP serves exclusively as a membrane anchoring subunit or further modulates RGS proteins to increase their GAP activity. To directly answer this question, we utilized a rapidly reversible chemically induced protein dimerization system that enabled us to control RGS localization independent from R7BP in living cells. To monitor kinetics of Gα deactivation, we coupled this strategy with measuring changes in the GAP activity by bioluminescence resonance energy transfer-based assay in a cellular system containing μ-opioid receptor. This approach was used to correlate changes in RGS localization and activity in the presence or absence of R7BP. Strikingly, we observed that RGS activity is augmented by membrane recruitment, in an orientation independent manner with no additional contributions provided by R7BP. These findings argue that the association of R7 RGS proteins with the membrane environment provides a major direct contribution to modulation of their GAP activity. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Inventory and analysis of ATP-binding cassette (ABC) systems in Brugia malayi.

Science.gov (United States)

Ardelli, B F; Stitt, L E; Tompkins, J B

2010-07-01

ABC systems are one of the largest described protein superfamilies. These systems have a domain organization that may contain 1 or more transmembrane domains (ABC_TM1F) and 1 or 2 ATP-binding domains (ABC_2). The functions (e.g., import, export and DNA repair) of these proteins distinguish the 3 classes of ABC systems. Mining and PCR-based cloning were used to identify 33 putative ABC systems from the Brugia malayi genome. There were 31 class 2 genes, commonly called ABC transporters, and 2 class 3 genes. The ABC transporters were divided into subfamilies. Three belonged to subfamily A, 16 to subfamily B, 5 to subfamily C, 1 to subfamily E and 3 to subfamilies F and G, respectively. None were placed in subfamilies D and H. Similar to other ABC systems, the ABC_2 domain of B. malayi genes was conserved and contained the Walker A and B motifs, the signature sequence/linker region and the switch region with the conserved histidine. The ABC_TM1F domain was less conserved. The relative abundance of ABC systems was quantified using real-time reverse transcription PCR and was significantly higher in female adults of B. malayi than in males and microfilaria, particularly those in subfamilies B and C, which are associated with drug resistance.

A family of metal-dependent phosphatases implicated in metabolite damage-control

Energy Technology Data Exchange (ETDEWEB)

Huang, Lili; Khusnutdinova, Anna; Nocek, Boguslaw; Brown, Greg; Xu, Xiaohui; Cui, Hong; Petit, Pierre; Flick, Robert; Zallot, Rémi; Balmant, Kelly; Ziemak, Michael J.; Shanklin, John; de Crécy-Lagard, Valérie; Fiehn, Oliver; Gregory, Jesse F.; Joachimiak, Andrzej; Savchenko, Alexei; Yakunin, Alexander F.; Hanson, Andrew D.

2016-06-20

DUF89 family proteins occur widely in both prokaryotes and eukaryotes, but their functions are unknown. Here we define three DUF89 subfamilies (I, II, and III), with subfamily II being split into stand-alone proteins and proteins fused to pantothenate kinase (PanK). We demonstrated that DUF89 proteins have metal-dependent phosphatase activity against reactive phosphoesters or their damaged forms, notably sugar phosphates (subfamilies II and III), phosphopantetheine and its S-sulfonate or sulfonate (subfamily II-PanK fusions), and nucleotides (subfamily I). Genetic and comparative genomic data strongly associated DUF89 genes with phosphoester metabolism. The crystal structure of the yeast (Saccharomyces cerevisiae) subfamily III protein YMR027W revealed a novel phosphatase active site with fructose 6-phosphate and Mg2+ bound near conserved signature residues Asp254 and Asn255 that are critical for activity. These findings indicate that DUF89 proteins are previously unrecognized hydrolases whose characteristic in vivo function is to limit potentially harmful buildups of normal or damaged phosphometabolites.

A tandem array of UDP-glycosyltransferases from the UGT73C subfamily glycosylate sapogenins, forming a spectrum of mono- and bisdesmosidic saponins.

Science.gov (United States)

Erthmann, Pernille Østerbye; Agerbirk, Niels; Bak, Søren

2018-05-01

This study identifies six UGT73Cs all able to glucosylate sapogenins at positions 3 and/or 28 which demonstrates that B. vulgaris has a much richer arsenal of UGTs involved in saponin biosynthesis than initially anticipated. The wild cruciferous plant Barbarea vulgaris is resistant to some insects due to accumulation of two monodesmosidic triterpenoid saponins, oleanolic acid 3-O-β-cellobioside and hederagenin 3-O-β-cellobioside. Insect resistance depends on the structure of the sapogenin aglycone and the glycosylation pattern. The B. vulgaris saponin profile is complex with at least 49 saponin-like metabolites, derived from eight sapogenins and including up to five monosaccharide units. Two B. vulgaris UDP-glycosyltransferases, UGT73C11 and UGT73C13, O-glucosylate sapogenins at positions 3 and 28, forming mainly 3-O-β-D-glucosides. The aim of this study was to identify UGTs responsible for the diverse saponin oligoglycoside moieties observed in B. vulgaris. Twenty UGT genes from the insect resistant genotype were selected and heterologously expressed in Nicotiana benthamiana and/or Escherichia coli. The extracts were screened for their ability to glycosylate sapogenins (oleanolic acid, hederagenin), the hormone 24-epibrassinolide and sapogenin monoglucosides (hederagenin and oleanolic acid 3-O-β-D-glucosides). Six UGTs from the UGT73C subfamily were able to glucosylate both sapogenins and both monoglucosides at positions 3 and/or 28. Some UGTs formed bisdesmosidic saponins efficiently. At least four UGT73C genes were localized in a tandem array with UGT73C11 and possibly UGT73C13. This organization most likely reflects duplication events followed by sub- and neofunctionalization. Indeed, signs of positive selection on several amino acid sites were identified and modelled to be localized on the UGT protein surface. This tandem array is proposed to initiate higher order bisdesmosidic glycosylation of B. vulgaris saponins, leading to the recently discovered

Gene : CBRC-GGOR-01-0100 [SEVENS

Lifescience Database Archive (English)

Full Text Available 98% ref|NP_001004479.1| olfactory receptor, family 11, subfamily H, member 4 [Homo sapiens] sp|Q8NGC9|O11H4_...transmembrane helix receptor [Homo sapiens] tpg|DAA04853.1| TPA_inf: olfactory receptor OR14-36 [Homo sapi...ens] gb|EAW66484.1| olfactory receptor, family 11, subfamily H, member 4 [Homo sapi...ens] gb|AAI37056.1| Olfactory receptor, family 11, subfamily H, member 4 [Homo sapiens] gb|AAI37055.1| Olfac...tory receptor, family 11, subfamily H, member 4 [Homo sapiens] dbj|BAI47453.1| ol

Protein (Cyanobacteria): 123924 [PGDBj - Ortholog DB

Lifescience Database Archive (English)

Full Text Available family enzyme, subfamily IA,REG-2-like HAD hydrolase, subfamily IA Leptolyngbya sp. PCC 7375 MTIPKVIFLDAVGTLFGVKGSVGEVYQALAQQAGVQASAH...ELDKAFYRSFAVANAMAFPGVPDVEIPHQEYLWWLAIAKDTFQRAGVFQEFSDFEVFFEGLYQHFATAAPWMVYQDTVNSLKR

Gene : CBRC-DNOV-01-0430 [SEVENS

Lifescience Database Archive (English)

Full Text Available _HUMAN 6e-67 50% ref|NP_112163.1| olfactory receptor, family 7, subfamily A, member 17 [Homo sapiens] sp|O14...581|OR7AH_HUMAN Olfactory receptor 7A17 gb|AAB82060.1| OLF4 [Homo sapiens] tpg|DAA04604.1| TPA_inf: olfactor...y receptor OR19-20 [Homo sapiens] gb|AAI01588.1| Olfactory receptor, family 7, su...bfamily A, member 17 [Homo sapiens] gb|AAI17358.1| Olfactory receptor, family 7, subfamily A, member 17 [Homo sapi...ens] gb|EAW84453.1| olfactory receptor, family 7, subfamily A, member 17 [Homo sapiens] 1e-65 50% MNSR

NCBI nr-aa BLAST: CBRC-GACU-17-0011 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-GACU-17-0011 ref|NP_005540.1| potassium voltage-gated channel, shaker-related ...4990.1| Potassium voltage-gated channel, shaker-related subfamily, member 10 [Homo sapiens] emb|CAH74103.1| ...potassium voltage-gated channel, shaker-related subfamily, member 10 [Homo sapien...s] gb|EAW56454.1| potassium voltage-gated channel, shaker-related subfamily, member 10 [Homo sapiens] NP_005540.1 0.0 62% ...

NCBI nr-aa BLAST: CBRC-FRUB-02-0329 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-FRUB-02-0329 ref|NP_005540.1| potassium voltage-gated channel, shaker-related ...4990.1| Potassium voltage-gated channel, shaker-related subfamily, member 10 [Homo sapiens] emb|CAH74103.1| ...potassium voltage-gated channel, shaker-related subfamily, member 10 [Homo sapien...s] gb|EAW56454.1| potassium voltage-gated channel, shaker-related subfamily, member 10 [Homo sapiens] NP_005540.1 0.0 66% ...

From Antarctica or Asia? New colonization scenario for Australian-New Guinean narrow mouth toads suggested from the findings on a mysterious genus Gastrophrynoides

OpenAIRE

Ahmad Norhayati; Yong Hoi-Sen; Belabut Daicus M; Matsui Masafumi; Kurabayashi Atsushi; Sudin Ahmad; Kuramoto Mitsuru; Hamidy Amir; Sumida Masayuki

2011-01-01

Abstract Background Microhylidae is a geographically widespread family of anurans. Although several extensive molecular analyses have attempted to elucidate their subfamilial relationships, and correlate these with Mesozoic and Cenozoic continental drifts, consensus has not been reached. Further, generic level relationships have not been well investigated in some microhylid subfamilies, and therefore subfamilial affiliations of some genera are still unclear. To elucidate the phylogenetic posi...

Molecular reconstruction of extinct LINE-1 elements and their interaction with nonautonomous elements.

Science.gov (United States)

Wagstaff, Bradley J; Kroutter, Emily N; Derbes, Rebecca S; Belancio, Victoria P; Roy-Engel, Astrid M

2013-01-01

Non-long terminal repeat retroelements continue to impact the human genome through cis-activity of long interspersed element-1 (LINE-1 or L1) and trans-mobilization of Alu. Current activity is dominated by modern subfamilies of these elements, leaving behind an evolutionary graveyard of extinct Alu and L1 subfamilies. Because Alu is a nonautonomous element that relies on L1 to retrotranspose, there is the possibility that competition between these elements has driven selection and antagonistic coevolution between Alu and L1. Through analysis of synonymous versus nonsynonymous codon evolution across L1 subfamilies, we find that the C-terminal ORF2 cys domain experienced a dramatic increase in amino acid substitution rate in the transition from L1PA5 to L1PA4 subfamilies. This observation coincides with the previously reported rapid evolution of ORF1 during the same transition period. Ancestral Alu sequences have been previously reconstructed, as their short size and ubiquity have made it relatively easy to retrieve consensus sequences from the human genome. In contrast, creating constructs of extinct L1 copies is a more laborious task. Here, we report our efforts to recreate and evaluate the retrotransposition capabilities of two ancestral L1 elements, L1PA4 and L1PA8 that were active ~18 and ~40 Ma, respectively. Relative to the modern L1PA1 subfamily, we find that both elements are similarly active in a cell culture retrotransposition assay in HeLa, and both are able to efficiently trans-mobilize Alu elements from several subfamilies. Although we observe some variation in Alu subfamily retrotransposition efficiency, any coevolution that may have occurred between LINEs and SINEs is not evident from these data. Population dynamics and stochastic variation in the number of active source elements likely play an important role in individual LINE or SINE subfamily amplification. If coevolution also contributes to changing retrotransposition rates and the progression of

Slipins: ancient origin, duplication and diversification of the stomatin protein family

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Young J Peter W

2008-02-01

Full Text Available Abstract Background Stomatin is a membrane protein that was first isolated from human red blood cells. Since then, a number of stomatin-like proteins have been identified in all three domains of life. The conservation among these proteins is remarkable, with bacterial and human homologs sharing 50 % identity. Despite being associated with a variety of diseases such as cancer, kidney failure and anaemia, precise functions of these proteins remain unclear. Results We have constructed a comprehensive phylogeny of all 'stomatin-like' sequences that share a 150 amino acid domain. We show these proteins comprise an ancient family that arose early in prokaryotic evolution, and we propose a new nomenclature that reflects their phylogeny, based on the name "slipin" (stomatin-like protein. Within prokaryotes there are two distinct subfamilies that account for the two different origins of the eight eukaryotic stomatin subfamilies, one of which gave rise to eukaryotic SLP-2, renamed here "paraslipin". This was apparently acquired through the mitochondrial endosymbiosis and is widely distributed amongst the major kingdoms. The other prokaryotic subfamily gave rise to the ancestor of the remaining seven eukaryotic subfamilies. The highly diverged "alloslipin" subfamily is represented only by fungal, viral and ciliate sequences. The remaining six subfamilies, collectively termed "slipins", are confined to metazoa. Protostome stomatin, as well as a newly reported arthropod subfamily slipin-4, are restricted to invertebrate groups, whilst slipin-1 (previously SLP-1 is present in nematodes and higher metazoa. In vertebrates, the stomatin family expanded considerably, with at least two duplication events giving rise to podocin and slipin-3 subfamilies (previously SLP-3, with the retained ancestral sequence giving rise to vertebrate stomatin. Conclusion Stomatin-like proteins have their origin in an ancient duplication event that occurred early on in the evolution

From Antarctica or Asia? New colonization scenario for Australian-New Guinean narrow mouth toads suggested from the findings on a mysterious genus Gastrophrynoides

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Ahmad Norhayati

2011-06-01

Full Text Available Abstract Background Microhylidae is a geographically widespread family of anurans. Although several extensive molecular analyses have attempted to elucidate their subfamilial relationships, and correlate these with Mesozoic and Cenozoic continental drifts, consensus has not been reached. Further, generic level relationships have not been well investigated in some microhylid subfamilies, and therefore subfamilial affiliations of some genera are still unclear. To elucidate the phylogenetic positions of two mysterious Asian genera, Gastrophrynoides and Phrynella, and to better understand the trans-continental distributions of microhylid taxa, we performed molecular phylogenetic and dating analyses using the largest molecular dataset applied to these taxa to date. Results Six nuclear and two mitochondrial genes (approx. 8 kbp were sequenced from 22 microhylid frog species representing eight subfamilies. The maximum likelihood and Bayesian analyses could not fully elucidate the subfamilial relationships, suggesting a rapid radiation of these taxa between 85 and 66 million years ago. In contrast, generic relationships of Asian microhylines were generally well resolved. Conclusion Our results clearly showed that one of two problematic Asian genera, Phrynella, was nested in the clade of the Asian subfamily Microhylinae. By contrast, Gastrophrynoides occupied the most basal position of the Australian-New Guinean subfamily Asterophryinae. The estimated divergence of Gastrophrynoides from other asterophryine was unexpectedly around 48 million years ago. Although a colonization scenario via Antarctica to the Australian-New Guinean landmass has been suggested for Asterophryinae, our finding suggested a novel colonization route via Indo-Eurasia.

2D or Not 2D? Testing the Utility of 2D Vs. 3D Landmark Data in Geometric Morphometrics of the Sculpin Subfamily Oligocottinae (Pisces; Cottoidea).

Science.gov (United States)

Buser, Thaddaeus J; Sidlauskas, Brian L; Summers, Adam P

2018-05-01

We contrast 2D vs. 3D landmark-based geometric morphometrics in the fish subfamily Oligocottinae by using 3D landmarks from CT-generated models and comparing the morphospace of the 3D landmarks to one based on 2D landmarks from images. The 2D and 3D shape variables capture common patterns across taxa, such that the pairwise Procrustes distances among taxa correspond and the trends captured by principal component analysis are similar in the xy plane. We use the two sets of landmarks to test several ecomorphological hypotheses from the literature. Both 2D and 3D data reject the hypothesis that head shape correlates significantly with the depth at which a species is commonly found. However, in taxa where shape variation in the z-axis is high, the 2D shape variables show sufficiently strong distortion to influence the outcome of the hypothesis tests regarding the relationship between mouth size and feeding ecology. Only the 3D data support previous studies which showed that large mouth sizes correlate positively with high percentages of elusive prey in the diet. When used to test for morphological divergence, 3D data show no evidence of divergence, while 2D data show that one clade of oligocottines has diverged from all others. This clade shows the greatest degree of z-axis body depth within Oligocottinae, and we conclude that the inability of the 2D approach to capture this lateral body depth causes the incongruence between 2D and 3D analyses. Anat Rec, 301:806-818, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Crystallization of the plant hormone receptors PYL9/RCAR1, PYL5/RCAR8 and PYR1/RCAR11 in the presence of (+)-abscisic acid

International Nuclear Information System (INIS)

Shibata, Nobuyuki; Kagiyama, Megumi; Nakagawa, Masahiro; Hirano, Yoshinori; Hakoshima, Toshio

2010-01-01

Crystals of the Arabidopsis abscisic acid receptors PYL9/RCAR1, PYL5/RCAR8 and PYR1/RCAR11 have been obtained. Abscisic acid (ABA) is a plant hormone that plays key regulatory roles in physiological pathways for the adaptation of vegetative tissues to abiotic stresses such as water stress in addition to events pertaining to plant growth and development. The Arabidopsis ABA receptor proteins PYR/PYLs/RCARs form a START family that contains 14 members which are classified into three subfamilies (I–III). Here, purification, crystallization and X-ray data collection are reported for a member of each of the subfamilies, PYL9/RCAR1 from subfamily I, PYL5/RCAR8 from subfamily II and PYR1/RCAR11 from subfamily III, in the presence of (+)-abscisic acid. The three proteins crystallize in space groups P3 1 21/P3 2 21, P2 and P1, respectively. X-ray intensity data were collected to 1.9–2.6 Å resolution

Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica).

Science.gov (United States)

Zhang, C H; Ma, R J; Shen, Z J; Sun, X; Korir, N K; Yu, M L

2014-04-08

In this study, 33 homeodomain-leucine zipper (HD-ZIP) genes were identified in peach using the HD-ZIP amino acid sequences of Arabidopsis thaliana as a probe. Based on the phylogenetic analysis and the individual gene or protein characteristics, the HD-ZIP gene family in peach can be classified into 4 subfamilies, HD-ZIP I, II, III, and IV, containing 14, 7, 4, and 8 members, respectively. The most closely related peach HD-ZIP members within the same subfamilies shared very similar gene structure in terms of either intron/exon numbers or lengths. Almost all members of the same subfamily shared common motif compositions, thereby implying that the HD-ZIP proteins within the same subfamily may have functional similarity. The 33 peach HD-ZIP genes were distributed across scaffolds 1 to 7. Although the primary structure varied among HD-ZIP family proteins, their tertiary structures were similar. The results from this study will be useful in selecting candidate genes from specific subfamilies for functional analysis.

Algal MIPs, high diversity and conserved motifs.

Science.gov (United States)

Anderberg, Hanna I; Danielson, Jonas Å H; Johanson, Urban

2011-04-21

Major intrinsic proteins (MIPs) also named aquaporins form channels facilitating the passive transport of water and other small polar molecules across membranes. MIPs are particularly abundant and diverse in terrestrial plants but little is known about their evolutionary history. In an attempt to investigate the origin of the plant MIP subfamilies, genomes of chlorophyte algae, the sister group of charophyte algae and land plants, were searched for MIP encoding genes. A total of 22 MIPs were identified in the nine analysed genomes and phylogenetic analyses classified them into seven subfamilies. Two of these, Plasma membrane Intrinsic Proteins (PIPs) and GlpF-like Intrinsic Proteins (GIPs), are also present in land plants and divergence dating support a common origin of these algal and land plant MIPs, predating the evolution of terrestrial plants. The subfamilies unique to algae were named MIPA to MIPE to facilitate the use of a common nomenclature for plant MIPs reflecting phylogenetically stable groups. All of the investigated genomes contained at least one MIP gene but only a few species encoded MIPs belonging to more than one subfamily. Our results suggest that at least two of the seven subfamilies found in land plants were present already in an algal ancestor. The total variation of MIPs and the number of different subfamilies in chlorophyte algae is likely to be even higher than that found in land plants. Our analyses indicate that genetic exchanges between several of the algal subfamilies have occurred. The PIP1 and PIP2 groups and the Ca2+ gating appear to be specific to land plants whereas the pH gating is a more ancient characteristic shared by all PIPs. Further studies are needed to discern the function of the algal specific subfamilies MIPA-E and to fully understand the evolutionary relationship of algal and terrestrial plant MIPs.

Algal MIPs, high diversity and conserved motifs

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Johanson Urban

2011-04-01

Full Text Available Abstract Background Major intrinsic proteins (MIPs also named aquaporins form channels facilitating the passive transport of water and other small polar molecules across membranes. MIPs are particularly abundant and diverse in terrestrial plants but little is known about their evolutionary history. In an attempt to investigate the origin of the plant MIP subfamilies, genomes of chlorophyte algae, the sister group of charophyte algae and land plants, were searched for MIP encoding genes. Results A total of 22 MIPs were identified in the nine analysed genomes and phylogenetic analyses classified them into seven subfamilies. Two of these, Plasma membrane Intrinsic Proteins (PIPs and GlpF-like Intrinsic Proteins (GIPs, are also present in land plants and divergence dating support a common origin of these algal and land plant MIPs, predating the evolution of terrestrial plants. The subfamilies unique to algae were named MIPA to MIPE to facilitate the use of a common nomenclature for plant MIPs reflecting phylogenetically stable groups. All of the investigated genomes contained at least one MIP gene but only a few species encoded MIPs belonging to more than one subfamily. Conclusions Our results suggest that at least two of the seven subfamilies found in land plants were present already in an algal ancestor. The total variation of MIPs and the number of different subfamilies in chlorophyte algae is likely to be even higher than that found in land plants. Our analyses indicate that genetic exchanges between several of the algal subfamilies have occurred. The PIP1 and PIP2 groups and the Ca2+ gating appear to be specific to land plants whereas the pH gating is a more ancient characteristic shared by all PIPs. Further studies are needed to discern the function of the algal specific subfamilies MIPA-E and to fully understand the evolutionary relationship of algal and terrestrial plant MIPs.

A framework for classification of prokaryotic protein kinases.

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Nidhi Tyagi

Full Text Available BACKGROUND: Overwhelming majority of the Serine/Threonine protein kinases identified by gleaning archaeal and eubacterial genomes could not be classified into any of the well known Hanks and Hunter subfamilies of protein kinases. This is owing to the development of Hanks and Hunter classification scheme based on eukaryotic protein kinases which are highly divergent from their prokaryotic homologues. A large dataset of prokaryotic Serine/Threonine protein kinases recognized from genomes of prokaryotes have been used to develop a classification framework for prokaryotic Ser/Thr protein kinases. METHODOLOGY/PRINCIPAL FINDINGS: We have used traditional sequence alignment and phylogenetic approaches and clustered the prokaryotic kinases which represent 72 subfamilies with at least 4 members in each. Such a clustering enables classification of prokaryotic Ser/Thr kinases and it can be used as a framework to classify newly identified prokaryotic Ser/Thr kinases. After series of searches in a comprehensive sequence database we recognized that 38 subfamilies of prokaryotic protein kinases are associated to a specific taxonomic level. For example 4, 6 and 3 subfamilies have been identified that are currently specific to phylum proteobacteria, cyanobacteria and actinobacteria respectively. Similarly subfamilies which are specific to an order, sub-order, class, family and genus have also been identified. In addition to these, we also identify organism-diverse subfamilies. Members of these clusters are from organisms of different taxonomic levels, such as archaea, bacteria, eukaryotes and viruses. CONCLUSION/SIGNIFICANCE: Interestingly, occurrence of several taxonomic level specific subfamilies of prokaryotic kinases contrasts with classification of eukaryotic protein kinases in which most of the popular subfamilies of eukaryotic protein kinases occur diversely in several eukaryotes. Many prokaryotic Ser/Thr kinases exhibit a wide variety of modular

Distribution and clonality of the vα and vβ T-cell receptor repertoire of regulatory T cells in leukemia patients with and without graft versus host disease.

Science.gov (United States)

Jin, Zhenyi; Wu, Xiuli; Chen, Shaohua; Yang, Lijian; Liu, Qifa; Li, Yangqiu

2014-03-01

Graft versus host disease (GVHD) is the main complication following allogeneic hematopoietic stem cell transplantation (allo-HSCT). Recent data indicated that regulatory T (Treg) cells might relate to GVHD, and such functions might be mediated by certain T-cell receptor (TCR) subfamily of Treg cells. Thus, we analyzed the distribution and clonality of the TCR Vα and Vβ repertoire of Treg cells from leukemia patients with and without GVHD after allo-HSCT. Numerous TCR Vα subfamilies, including Vα1, Vα9, Vα13, Vα16-19, and Vα24-29, were absent in Treg cells after allo-HSCT. The usage numbers for the TCR Vα and Vβ subfamilies in Treg cells from patients without GVHD appeared more widely. The expression frequencies of Vα10 or Vα20 between both groups were significantly different. Moreover, the expression frequency of TCR Vβ2 subfamily in patients without GVHD was significantly higher than that in patients with GVHD. Oligoclonally expanded TCR Vα and Vβ Treg cells were identified in a few samples in both groups. Restricted utilization of the Vα and Vβ subfamilies and the absence of some important TCR rearrangements in Treg cells may be related to GVHD due to a lower regulating function of Treg subfamilies.

The Mite Larvae of the family Trombiculidae in the Oudemans collection: Taxonomy and Medical importance1)

NARCIS (Netherlands)

Fuller, H.S.

1952-01-01

Introduction............... 2 General Remarks.............. 3 Methods of Study............. 6 Acknowledgements............. 9 Family Trombiculidae............. 11 Key to Subfamilies............. 13 Subfamily Trombiculinae Ewing........... 14 Key to Genera.............. 14 Genus Trombicula

Aquaporins in Digestive System.

Science.gov (United States)

Zhu, Shuai; Ran, Jianhua; Yang, Baoxue; Mei, Zhechuan

2017-01-01

In this chapter, we mainly discuss the expression and function of aquaporins (AQPs ) expressed in digestive system . AQPs in gastrointestinal tract include four members of aquaporin subfamily: AQP1, AQP4, AQP5 and AQP8, and a member of aquaglyceroporin subfamily: AQP3. In the digestive glands, especially the liver, we discuss three members of aquaporin subfamily: AQP1, AQP5 and AQP8, a member of aquaglyceroporin subfamily: AQP9. AQP3 is involved in the diarrhea and inflammatory bowel disease; AQP5 is relevant to gastric carcinoma cell proliferation and migration; AQP9 plays considerable role in glycerol metabolism , urea transport and hepatocellular carcinoma. Further investigation is necessary for specific locations and functions of AQPs in digestive system.

Characterization of the Paenibacillus beijingensis DSM 24997 GtfD and its glucan polymer products representing a new glycoside hydrolase 70 subfamily of 4,6-α-glucanotransferase enzymes.

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Joana Gangoiti

Full Text Available Previously we have reported that the Gram-negative bacterium Azotobacter chroococcum NCIMB 8003 uses the 4,6-α-glucanotransferase GtfD to convert maltodextrins and starch into a reuteran-like polymer consisting of (α1→4 glucan chains connected by alternating (α1→4/(α1→6 linkages and (α1→4,6 branching points. This enzyme constituted the single evidence for this reaction and product specificity in the GH70 family, mostly containing glucansucrases encoded by lactic acid bacteria (http://www.CAZy.org. In this work, 4 additional GtfD-like proteins were identified in taxonomically diverse plant-associated bacteria forming a new GH70 subfamily with intermediate characteristics between the evolutionary related GH13 and GH70 families. The GtfD enzyme encoded by Paenibacillus beijingensis DSM 24997 was characterized providing the first example of a reuteran-like polymer synthesizing 4,6-α-glucanotransferase in a Gram-positive bacterium. Whereas the A. chroococcum GtfD activity on amylose resulted in the synthesis of a high molecular polymer, in addition to maltose and other small oligosaccharides, two reuteran-like polymer distributions are produced by P. beijingensis GtfD: a high-molecular mass polymer and a low-molecular mass polymer with an average Mw of 27 MDa and 19 kDa, respectively. Compared to the A. chroooccum GtfD product, both P. beijingensis GtfD polymers contain longer linear (α1→4 sequences in their structure reflecting a preference for transfer of even longer glucan chains by this enzyme. Overall, this study provides new insights into the evolutionary history of GH70 enzymes, and enlarges the diversity of natural enzymes that can be applied for modification of the starch present in food into less and/or more slowly digestible carbohydrate structures.

ATP-binding cassette subfamily A, member 4 intronic variants c.4773+3A>G and c.5461-10T>C cause Stargardt disease due to defective splicing.

Science.gov (United States)

Jonsson, Frida; Westin, Ida Maria; Österman, Lennart; Sandgren, Ola; Burstedt, Marie; Holmberg, Monica; Golovleva, Irina

2018-02-20

Inherited retinal dystrophies (IRDs) represent a group of progressive conditions affecting the retina. There is a great genetic heterogeneity causing IRDs, and to date, more than 260 genes are associated with IRDs. Stargardt disease, type 1 (STGD1) or macular degeneration with flecks, STGD1 represents a disease with early onset, central visual impairment, frequent appearance of yellowish flecks and mutations in the ATP-binding cassette subfamily A, member 4 (ABCA4) gene. A large number of intronic sequence variants in ABCA4 have been considered pathogenic although their functional effect was seldom demonstrated. In this study, we aimed to reveal how intronic variants present in patients with Stargardt from the same Swedish family affect splicing. The splicing of the ABCA4 gene was studied in human embryonic kidney cells, HEK293T, and in human retinal pigment epithelium cells, ARPE-19, using a minigene system containing variants c.4773+3A>G and c.5461-10T>C. We showed that both ABCA4 variants, c.4773+3A>G and c.5461-10T>C, cause aberrant splicing of the ABCA4 minigene resulting in exon skipping. We also demonstrated that splicing of ABCA4 has different outcomes depending on transfected cell type. Two intronic variants c.4773+3A>G and c.5461-10T>C, both predicted to affect splicing, are indeed disease-causing mutations due to skipping of exons 33, 34, 39 and 40 of ABCA4 gene. The experimental proof that ABCA4 mutations in STGD patients affect protein function is crucial for their inclusion to future clinical trials; therefore, functional testing of all ABCA4 intronic variants associated with Stargardt disease by minigene technology is desirable. © 2018 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

The reprogramming factor nuclear receptor subfamily 5, group A, member 2 cannot replace octamer-binding transcription factor 4 function in the self-renewal of embryonic stem cells.

Science.gov (United States)

Choi, Kyeng-Won; Oh, Hye-Rim; Lee, Jaeyoung; Lim, Bobae; Han, Yong-Mahn; Oh, Junseo; Kim, Jungho

2014-02-01

Although octamer-binding transcription factor 4 (Oct-4) is one of the most intensively studied factors in mammalian development, no cellular genes capable of replacing Oct-4 function in embryonic stem (ES) cells have been found. Recent data show that nuclear receptor subfamily 5, group A, member 2 (Nr5a2) is able to replace Oct-4 function in the reprogramming process; however, it is unclear whether Nr5a2 can replace Oct-4 function in ES cells. In this study, the ability of Nr5a2 to maintain self-renewal and pluripotency in ES cells was investigated. Nr5a2 localized to the nucleus in ES cells, similarly to Oct-4. However, expression of Nr5a2 failed to rescue the stem cell phenotype or to maintain the self-renewal ability of ES cells. Furthermore, as compared with Oct-4-expressing ES cells, Nr5a2-expressing ES cells showed a reduced number of cells in S-phase, did not expand normally, and did not remain in an undifferentiated state. Ectopic expression of Nr5a2 in ES cells was not able to activate transcription of ES cell-specific genes, and gene expression profiling demonstrated differences between Nr5a2-expressing and Oct-4-expressing ES cells. In addition, Nr5a2-expressing ES cells were not able to form teratomas in nude mice. Taken together, these results strongly suggest that the gene regulation properties of Nr5a2 and Oct-4 and their abilities to confer self-renewal and pluripotency of ES cells differ. The present study provides strong evidence that Nr5a2 cannot replace Oct-4 function in ES cells. © 2013 FEBS.

Analysis of CR1 Repeats in the Zebra Finch Genome

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George E. Liu

2013-06-01

Full Text Available Most bird species have smaller genomes and fewer repeats than mammals. Chicken Repeat 1 (CR1 repeat is one of the most abundant families of repeats, ranging from ~133,000 to ~187,000 copies accounting for ~50 to ~80% of the interspersed repeats in the zebra finch and chicken genomes, respectively. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to multiple CR1 subfamilies in the chicken. In this study, we performed a global assessment of the divergence distributions, phylogenies, and consensus sequences of CR1 repeats in the zebra finch genome. We identified and validated 34 CR1 subfamilies and further analyzed the correlation between these subfamilies. We also discovered 4 novel lineage-specific CR1 subfamilies in the zebra finch when compared to the chicken genome. We built various evolutionary trees of these subfamilies and concluded that CR1 repeats may play an important role in reshaping the structure of bird genomes.

Genome-wide analysis of the GRAS gene family in physic nut (Jatropha curcas L.).

Science.gov (United States)

Wu, Z Y; Wu, P Z; Chen, Y P; Li, M R; Wu, G J; Jiang, H W

2015-12-29

GRAS proteins play vital roles in plant growth and development. Physic nut (Jatropha curcas L.) was found to have a total of 48 GRAS family members (JcGRAS), 15 more than those found in Arabidopsis. The JcGRAS genes were divided into 12 subfamilies or 15 ancient monophyletic lineages based on the phylogenetic analysis of GRAS proteins from both flowering and lower plants. The functions of GRAS genes in 9 subfamilies have been reported previously for several plants, while the genes in the remaining 3 subfamilies were of unknown function; we named the latter families U1 to U3. No member of U3 subfamily is present in Arabidopsis and Poaceae species according to public genome sequence data. In comparison with the number of GRAS genes in Arabidopsis, more were detected in physic nut, resulting from the retention of many ancient GRAS subfamilies and the formation of tandem repeats during evolution. No evidence of recent duplication among JcGRAS genes was observed in physic nut. Based on digital gene expression data, 21 of the 48 genes exhibited differential expression in four tissues analyzed. Two members of subfamily U3 were expressed only in buds and flowers, implying that they may play specific roles. Our results provide valuable resources for future studies on the functions of GRAS proteins in physic nut.

Gene conversion as a secondary mechanism of short interspersed element (SINE) evolution

Energy Technology Data Exchange (ETDEWEB)

Kass, D.H. [Louisiana State Univ. Medical Center, New Orleans, LA (United States). Dept. of Biochemistry and Molecular Biology; Batzer, M.A. [Lawrence Livermore National Lab., CA (United States); Deininger, P.L. [Louisiana State Univ. Medical Center, New Orleans, LA (United States). Dept. of Biochemistry and Molecular Biology]|[Alton Ochsner Medical Foundation, New Orleans, LA (United States). Lab. of Molecular Genetics

1995-01-01

The Alu repetitive family of short interspersed elements (SINEs) in primates can be subdivided into distinct subfamilies by specific diagnostic nucleotide changes. The older subfamilies are generally very abundant, while the younger subfamilies have fewer copies. Some of the youngest Alu elements are absent in the orthologous loci of nonhuman primates, indicative of recent retroposition events, the primary mode of SINE evolutions. PCR analysis of one young Alu subfamily (Sb2) member found in the low-density lipoprotein receptor gene apparently revealed the presence of this element in the green monkey, orangutan, gorilla, and chimpanzee genomes, as well as the human genome. However, sequence analysis of these genomes revealed a highly mutated, older, primate-specific Alu element was present at this position in the nonhuman primates. Comparison of the flanking DNA sequences upstream of this Alu insertion corresponded to evolution expected for standard primate phylogeny, but comparison of the Alu repeat sequences revealed that the human element departed from this phylogeny. The change in the human sequence apparently occurred by a gene conversion event only within the Alu element itself, converting it from one of the oldest to one of the youngest Alu subfamilies. Although gene conversions of Alu elements are clearly very rare, this finding shows that such events can occur and contribute to specific cases of SINE subfamily evolution.

Taxonomia da subfamília Corinninae (Araneae, Corinnidae nas regiões neotropical e neártica Taxonomy of the subfamily Corinninae (Araneae, Corinnidae in neotropical and neartic regions

Directory of Open Access Journals (Sweden)

Alexandre Bragio Bonaldo

2000-11-01

Full Text Available The subfamily Corinninae is characterized and diagnosed. Two synapomorphies are hypothesized for the subfamily, both regarding the male palpal reservoir, which is primarily coiled and presents a sclerotized distal sector. Seventeen genera are recognized, six of which are new: Abapeba (type species Corinna lacertosa Simon, Erendira (type species Corinna pallidoguttata Simon, Septentrinna (type species Corinna bicalcarata Simon, Simonestus (type species Diestus validus Simon, Tapixaua (type species T. callida sp. nov. and Tupirinna (type species T. rosae sp. nov.. The genera Creugas Thorell, Falconina Brignoli and Paradiestus Mello-Leitão are revalidated. Diestus Simon and Lausus Simon are newly synonymized with Corinna C. L. Koch. Chemmis Simon is included in the synonymy of Megalostrata Karsch. Hypsinotus L. Koch is removed from the synonymy of Corinna and included in the synonymy of Creugas. Thirteen new species are described: Septentrinna yucatan and S. potosi from Mexico; Tupirinna rosae from Venezuela and Brazil; Tapixaua callida from Brazil and Peru; Abapeba hoeferi, A. rioclaro, A. taruma, Corinna ducke, C. colombo, C. mourai, C. recurva and Parachemmis manauara from Brazil; Creugas lisei from Brazil, Argentina and Uruguay. Twenty seven species are redescribed. Fifty eight new combinations are presented: from Chemmis, Septentrinna steckleri (Gertsch; from Corinna, Abapeba abalosi (Mello-Leitão, A. cleonei (Petrunkevitch, A. echinus (Simon, A. grassima (Chickering, A. guanicae (Petrunkevitch, A. lacertosa (Simon, A. luctuosa (F. O. Pickard-Cambridge, A. lugubris (Schenkel, A. pennata (Caporiacco, A. kochi (Petrunkevitch, A. saga (F. O. Pickard-Cambridge, A. wheeleri (Petrunkevitch, Creugas annamae (Gertsch & Davis, C. apophysarius (Caporiacco, C. bajulus (Gertsch, C. bellator (L. Koch, C. bicuspis (F.O. Pickard-Cambridge, C. epicureanus (Chamberlin, C. falculus (F. O. Pickard-Cambridge, C. mucronatus (F. O. Pickard-Cambridge, C. navus (F

The domain architecture of large guanine nucleotide exchange factors for the small GTP-binding protein Arf

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Geldner Niko

2005-02-01

Full Text Available Abstract Background Small G proteins, which are essential regulators of multiple cellular functions, are activated by guanine nucleotide exchange factors (GEFs that stimulate the exchange of the tightly bound GDP nucleotide by GTP. The catalytic domain responsible for nucleotide exchange is in general associated with non-catalytic domains that define the spatio-temporal conditions of activation. In the case of small G proteins of the Arf subfamily, which are major regulators of membrane trafficking, GEFs form a heterogeneous family whose only common characteristic is the well-characterized Sec7 catalytic domain. In contrast, the function of non-catalytic domains and how they regulate/cooperate with the catalytic domain is essentially unknown. Results Based on Sec7-containing sequences from fully-annotated eukaryotic genomes, including our annotation of these sequences from Paramecium, we have investigated the domain architecture of large ArfGEFs of the BIG and GBF subfamilies, which are involved in Golgi traffic. Multiple sequence alignments combined with the analysis of predicted secondary structures, non-structured regions and splicing patterns, identifies five novel non-catalytic structural domains which are common to both subfamilies, revealing that they share a conserved modular organization. We also report a novel ArfGEF subfamily with a domain organization so far unique to alveolates, which we name TBS (TBC-Sec7. Conclusion Our analysis unifies the BIG and GBF subfamilies into a higher order subfamily, which, together with their being the only subfamilies common to all eukaryotes, suggests that they descend from a common ancestor from which species-specific ArfGEFs have subsequently evolved. Our identification of a conserved modular architecture provides a background for future functional investigation of non-catalytic domains.

A meningococcal NOMV-FHbp vaccine for Africa elicits broader serum bactericidal antibody responses against serogroup B and non-B strains than a licensed serogroup B vaccine.

Science.gov (United States)

Pajon, Rolando; Lujan, Eduardo; Granoff, Dan M

2016-01-27

Meningococcal epidemics in Sub-Sahara caused by serogroup A strains are controlled by a group A polysaccharide conjugate vaccine. Strains with serogroups C, W and X continue to cause epidemics. Protein antigens in licensed serogroup B vaccines are shared among serogroup B and non-B strains. Compare serum bactericidal antibody responses elicited by an investigational native outer membrane vesicle vaccine with over-expressed Factor H binding protein (NOMV-FHbp) and a licensed serogroup B vaccine (MenB-4C) against African serogroup A, B, C, W and X strains. Human Factor H (FH) transgenic mice were immunized with NOMV-FHbp prepared from a mutant African meningococcal strain containing genetically attenuated endotoxin and a mutant sub-family B FHbp antigen with low FH binding, or with MenB-4C, which contains a recombinant sub-family B FHbp antigen that binds human FH, and three other antigens, NHba, NadA and PorA P1.4, capable of eliciting bactericidal antibody. The NOMV-FHbp elicited serum bactericidal activity against 12 of 13 serogroup A, B, W or X strains from Africa, and four isogenic serogroup B mutants with sub-family B FHbp sequence variants. There was no activity against a serogroup B mutant with sub-family A FHbp, or two serogroup C isolates from a recent outbreak in Northern Nigeria, which were mismatched for both PorA and sub-family of the FHbp vaccine antigen. For MenB-4C, NHba was expressed by all 16 African isolates tested, FHbp sub-family B in 13, and NadA in five. However, MenB-4C elicited titers ≥ 1:10 against only one isolate, and against only two of four serogroup B mutant strains with sub-family B FHbp sequence variants. NOMV-FHbp has greater potential to confer serogroup-independent protection in Africa than the licensed MenB-4C vaccine. However, the NOMV-FHbp vaccine will require inclusion of sub-family A FHbp for coverage against recent serogroup C strains causing outbreaks in Northern Nigeria. Copyright © 2015 Elsevier Ltd. All rights

New Korean Record of Twenty Eight Species of the Family Ichneumonidae (Hymenoptera

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Choi, Jin-Kyung

2014-04-01

Full Text Available We report twenty eight ichneumonid species new to Korea. These species belong to seven subfamilies. Among them five subfamilies, Diacritinae Townes, 1965, Microleptinae Townes, 1958, Orthocentrinae F$\\ddot{o} $ 수식 이미지rster, 1869, Orthopelmatinae Schmiedeknecht, 1910, Phrudinae Townes and Townes, 1949, are newly introduced to Korean fauna. All specimens are based on the insect collection of animal systematic laboratory at the Yeungnam University Gyeongsan Campus. Photographs of habitus of newly recorded subfamilies, diagnosis of 28 species and host information are provided.

Acetate formation in the energy metabolism of parasitic helminths and protists.

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Tielens, Aloysius G M; van Grinsven, Koen W A; Henze, Katrin; van Hellemond, Jaap J; Martin, William

2010-03-15

Formation and excretion of acetate as a metabolic end product of energy metabolism occurs in many protist and helminth parasites, such as the parasitic helminths Fasciola hepatica, Haemonchus contortus and Ascaris suum, and the protist parasites, Giardia lamblia, Entamoeba histolytica, Trichomonas vaginalis as well as Trypanosoma and Leishmania spp. In all of these parasites acetate is a main end product of their energy metabolism, whereas acetate formation does not occur in their mammalian hosts. Acetate production might therefore harbour novel targets for the development of new anti-parasitic drugs. In parasites, acetate is produced from acetyl-CoA by two different reactions, both involving substrate level phosphorylation, that are catalysed by either a cytosolic acetyl-CoA synthetase (ACS) or an organellar acetate:succinate CoA-transferase (ASCT). The ACS reaction is directly coupled to ATP synthesis, whereas the ASCT reaction yields succinyl-CoA for ATP formation via succinyl-CoA synthetase (SCS). Based on recent work on the ASCTs of F. hepatica, T. vaginalis and Trypanosoma brucei we suggest the existence of three subfamilies of enzymes within the CoA-transferase family I. Enzymes of these three subfamilies catalyse the ASCT reaction in eukaryotes via the same mechanism, but the subfamilies share little sequence homology. The CoA-transferases of the three subfamilies are all present inside ATP-producing organelles of parasites, those of subfamily IA in the mitochondria of trypanosomatids, subfamily IB in the mitochondria of parasitic worms and subfamily IC in hydrogenosome-bearing parasites. Together with the recent characterisation among non-parasitic protists of yet a third route of acetate formation involving acetate kinase (ACK) and phosphotransacetylase (PTA) that was previously unknown among eukaryotes, these recent developments provide a good opportunity to have a closer look at eukaryotic acetate formation. (c) 2010 Australian Society for Parasitology

Bossa Nova: Introducing modularity into the Bossa Nova domain-specific language

DEFF Research Database (Denmark)

Lawall, Julia Laetitia; Duschene, Hervé; Muller, Gilles

2005-01-01

subfamilies in using this language to implement an encyclopedic, multi-OS library of scheduling policies. In this paper, we propose that introducing certain kinds of modularity into the language can furnish abstractions appropriate for implementing scheduling policy subfamilies. We present the design of our...... of how to capture these subfamilies in DSL abstractions. A solution should retain features of the original DSL to leverage existing expertise and support tools.   The Bossa DSL is a language targeted towards the development of kernel process scheduling policies. We have encountered the issue of program...

De Larven der Nederlandse Chironomidae (Diptera) : Orthocladiinae sensu lato

NARCIS (Netherlands)

Moller Pillot, H.K.M.

1984-01-01

Systematiek De indeling van de Orthocladiinae levert zo mogelijk nog meer problemen op dan die van de andere subfamilies van de Chironomidae. Momenteel is het algemeen gebruikelijk de groep in vier subfamilies te splitsen: Diamesinae, Prodiamesinae, Orthocladiinae en Telmatogetoninae (zie bijv.

NCBI nr-aa BLAST: CBRC-CPOR-01-0502 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-CPOR-01-0502 ref|NP_989793.1| potassium voltage-gated channel, shaker-related ...subfamily, member 10 [Gallus gallus] gb|AAP94024.1| shaker subfamily potassium channel KCNA10 [Gallus gallus] NP_989793.1 0.0 78% ...

NCBI nr-aa BLAST: CBRC-OLAT-07-0019 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-OLAT-07-0019 ref|NP_989793.1| potassium voltage-gated channel, shaker-related ...subfamily, member 10 [Gallus gallus] gb|AAP94024.1| shaker subfamily potassium channel KCNA10 [Gallus gallus] NP_989793.1 0.0 72% ...

NCBI nr-aa BLAST: CBRC-FRUB-02-0329 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-FRUB-02-0329 ref|NP_989793.1| potassium voltage-gated channel, shaker-related ...subfamily, member 10 [Gallus gallus] gb|AAP94024.1| shaker subfamily potassium channel KCNA10 [Gallus gallus] NP_989793.1 0.0 71% ...

Upregulated Expression of Transient Receptor Potential Cation Channel Subfamily V Receptors in Mucosae of Patients with Oral Squamous Cell Carcinoma and Patients with a History of Alcohol Consumption or Smoking.

Science.gov (United States)

Sakakibara, Akiko; Sakakibara, Shunsuke; Kusumoto, Junya; Takeda, Daisuke; Hasegawa, Takumi; Akashi, Masaya; Minamikawa, Tsutomu; Hashikawa, Kazunobu; Terashi, Hiroto; Komori, Takahide

2017-01-01

Transient receptor potential cation channel (subfamily V, members 1-4) (TRPV1-4) are expressed in skin and neurons and activated by external stimuli in normal mucosae of all oral cavity sites. The oral cavity is exposed to various stimuli, including temperature, mechanical stimuli, chemical substances, and changes in pH, and, notably, the risk factors for oncogenic transformation in oral squamous epithelium are the same as the external stimuli received by TRPV1-4 receptors. Hence, we examined the relationship between oral squamous cell carcinoma (SCC) and TRPV1-4 expression. Oral SCC patients (n = 37) who underwent surgical resection were included in this study. We investigated the expression of TRPV1-4 by immunohistochemical staining and quantification of TRPV1-4 mRNA in human oral mucosa. In addition, we compared the TRPV1-4 levels in mucosa from patients with SCC to those in normal oral mucosa. The receptors were expressed in oral mucosa at all sites (tongue, buccal mucosa, gingiva, and oral floor) and the expression was stronger in epithelia from patients with SCC than in normal epithelia. Furthermore, alcohol consumption and tobacco use were strongly associated with the occurrence of oral cancer and were found to have a remarkable influence on TRPV1-4 receptor expression in normal oral mucosa. In particular, patients with a history of alcohol consumption demonstrated significantly higher expression levels. Various external stimuli may influence the behavior of cancer cells. Overexpression of TRPV1-4 is likely to be a factor in enhanced sensitivity to external stimuli. These findings could contribute to the establishment of novel strategies for cancer therapy or prevention.

NCBI nr-aa BLAST: CBRC-GACU-17-0012 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-GACU-17-0012 ref|NP_001025549.1| potassium voltage-gated channel, shaker-relat...ed subfamily, member 3 [Gallus gallus] gb|AAP94028.1| shaker subfamily potassium channel Kv1.3 [Gallus gallus] NP_001025549.1 0.0 74% ...

NCBI nr-aa BLAST: CBRC-TGUT-29-0000 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-TGUT-29-0000 ref|NP_001025549.1| potassium voltage-gated channel, shaker-relat...ed subfamily, member 3 [Gallus gallus] gb|AAP94028.1| shaker subfamily potassium channel Kv1.3 [Gallus gallus] NP_001025549.1 0.0 98% ...

NCBI nr-aa BLAST: CBRC-TNIG-09-0017 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-TNIG-09-0017 ref|NP_001025549.1| potassium voltage-gated channel, shaker-relat...ed subfamily, member 3 [Gallus gallus] gb|AAP94028.1| shaker subfamily potassium channel Kv1.3 [Gallus gallus] NP_001025549.1 0.0 83% ...

NCBI nr-aa BLAST: CBRC-FRUB-02-0328 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-FRUB-02-0328 ref|NP_001025549.1| potassium voltage-gated channel, shaker-relat...ed subfamily, member 3 [Gallus gallus] gb|AAP94028.1| shaker subfamily potassium channel Kv1.3 [Gallus gallus] NP_001025549.1 0.0 84% ...

NCBI nr-aa BLAST: CBRC-XTRO-01-2371 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-XTRO-01-2371 ref|NP_001025549.1| potassium voltage-gated channel, shaker-relat...ed subfamily, member 3 [Gallus gallus] gb|AAP94028.1| shaker subfamily potassium channel Kv1.3 [Gallus gallus] NP_001025549.1 0.0 78% ...

NCBI nr-aa BLAST: CBRC-OLAT-07-0020 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-OLAT-07-0020 ref|NP_001025549.1| potassium voltage-gated channel, shaker-relat...ed subfamily, member 3 [Gallus gallus] gb|AAP94028.1| shaker subfamily potassium channel Kv1.3 [Gallus gallus] NP_001025549.1 0.0 76% ...

NCBI nr-aa BLAST: CBRC-DRER-06-0073 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-DRER-06-0073 ref|NP_001025549.1| potassium voltage-gated channel, shaker-relat...ed subfamily, member 3 [Gallus gallus] gb|AAP94028.1| shaker subfamily potassium channel Kv1.3 [Gallus gallus] NP_001025549.1 0.0 74% ...

NCBI nr-aa BLAST: CBRC-OLAT-26-0139 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-OLAT-26-0139 ref|NP_001025549.1| potassium voltage-gated channel, shaker-relat...ed subfamily, member 3 [Gallus gallus] gb|AAP94028.1| shaker subfamily potassium channel Kv1.3 [Gallus gallus] NP_001025549.1 0.0 81% ...

NCBI nr-aa BLAST: CBRC-ACAR-01-1044 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-ACAR-01-1044 ref|NP_001025549.1| potassium voltage-gated channel, shaker-relat...ed subfamily, member 3 [Gallus gallus] gb|AAP94028.1| shaker subfamily potassium channel Kv1.3 [Gallus gallus] NP_001025549.1 0.0 90% ...

NCBI nr-aa BLAST: CBRC-DRER-26-0215 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-DRER-26-0215 ref|NP_001025549.1| potassium voltage-gated channel, shaker-relat...ed subfamily, member 3 [Gallus gallus] gb|AAP94028.1| shaker subfamily potassium channel Kv1.3 [Gallus gallus] NP_001025549.1 0.0 74% ...

Antigenic and genetic variability of human metapneumoviruses

NARCIS (Netherlands)

S. Herfst (Sander); L. Sprong; P.A. Cane; E. Forleo-Neto; A.D.M.E. Osterhaus (Albert); R.A.M. Fouchier (Ron); R.L. de Swart (Rik); B.G. van den Hoogen (Bernadette)

2004-01-01

textabstractHuman metapneumovirus (HMPV) is a member of the subfamily Pneumovirinae within the family Paramyxo- viridae. Other members of this subfamily, respiratory syncytial virus and avian pneumovirus, can be divided into subgroups on the basis of genetic or antigenic differences or both. For

Comprehensive behavioral analysis of mice deficient in Rapgef2 and Rapgef6, a subfamily of guanine nucleotide exchange factors for Rap small GTPases possessing the Ras/Rap-associating domain.

Science.gov (United States)

Maeta, Kazuhiro; Hattori, Satoko; Ikutomo, Junji; Edamatsu, Hironori; Bilasy, Shymaa E; Miyakawa, Tsuyoshi; Kataoka, Tohru

2018-05-10

Rapgef2 and Rapgef6 define a subfamily of guanine nucleotide exchange factors for Rap small GTPases, characterized by the possession of the Ras/Rap-associating domain. Previous genomic analyses suggested their possible involvement in the etiology of schizophrenia. We recently demonstrated the development of an ectopic cortical mass (ECM), which resembles the human subcortical band heterotopia, in the dorsal telencephalon-specific Rapgef2 conditional knockout (Rapgef2-cKO) brains. Additional knockout of Rapgef6 in Rapgef2-cKO mice resulted in gross enlargement of the ECM whereas knockout of Rapgef6 alone (Rapgef6-KO) had no discernible effect on the brain morphology. Here, we performed a battery of behavioral tests to examine the effects of Rapgef2 or Rapgef6 deficiency on higher brain functions. Rapgef2-cKO mice exhibited hyperlocomotion phenotypes. They showed decreased anxiety-like behavior in the elevated plus maze and the open-field tests as well as increased depression-like behavior in the Porsolt forced swim and tail suspension tests. They also exhibited increased sociability especially in novel environments. They showed defects in cognitive function as evidenced by reduced learning ability in the Barnes circular maze test and by impaired working memory in the T maze tests. In contrast, although Rapgef6 and Rapgef2 share similarities in biochemical roles, Rapgef6-KO mice exhibited mild behavioral abnormalities detected with a number of behavioral tests, such as hyperlocomotion phenotype in the open-field test and the social interaction test with a novel environment and working-memory defects in the T-maze test. In conclusion, although there were differences in their brain morphology and the magnitude of the behavioral abnormalities, Rapgef2-cKO mice and Rapgef6-KO mice exhibited hyperlocomotion phenotype and working-memory defect, both of which could be recognized as schizophrenia-like behavior.

Checklist of butterfly fauna of Kohat, Khyber Pakhtunkhwa, Pakistan

Directory of Open Access Journals (Sweden)

Farzana Perveen

2012-09-01

Full Text Available The butterflies play dual role, firstly as the pollinator, carries pollen from one flower to another and secondly their larvae act as the pest, injurious to various crops. Their 21 species were identified belonging to 3 different families from Kohat, Pakistan during September-December 2008. The reported families Namphalidae covered 33%, Papilionidae 10%, and Pieridae 57% biodiversity of butterflies of Kohat. In Namphalidae included: species belonging to subfamily Nymphalinae, Indian fritillary, Argynnis hyperbius Linnaeus; common castor, Ariadne merione (Cramer; painted lady, Cynthia cardui (Linnaeus; peacock pansy, Junonia almanac Linnaeus; blue pansy, J. orithya Linnaeus; common leopard, Phalantha phalantha (Drury; species belonging to subfamily Satyrinae, white edged rock brown, Hipparchia parisatis (Kollar. In Papilionidae included: subfamily Papilioninae, lime butterfly, Papilio demoleus Linnaeus and common mormon, Pa. polytes Linnaeus. In Pieridae included: subfamily Coliaclinae, dark clouded yellow, Colias croceus (Geoffroy; subfamily Coliadinae, lemon emigrant, Catopsilia pomona Fabricius; little orange tip, C. etrida Boisduval; blue spot arab,Colotis protractus Butler; common grass yellow, Eumera hecab (Linnaeus; common brimstone, Gonepteryx rhamni (Linnaeus; yellow orange tip, Ixias pyrene Linnaeus; subfamily Pierinae, pioneer white butterfly, Belenoi aurota Bingham; Murree green-veined white, Pieris ajaka Moore; large cabbage white, P. brassicae Linnaeus; green-veined white, P. napi (Linnaeus; small cabbage white, P. rapae Linnaeus. The wingspan of collected butterflies, minimum was 25 mm of C. etrida which was the smallest butterfly, however, maximum was 100 mm of P. demoleus and P. polytes which were the largest butterflies. A detail study is required for further exploration of butterflies' fauna of Kohat.

Genome-wide analysis of the human Alu Yb-lineage

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Carter Anthony B

2004-03-01

Full Text Available Abstract The Alu Yb-lineage is a 'young' primarily human-specific group of short interspersed element (SINE subfamilies that have integrated throughout the human genome. In this study, we have computationally screened the draft sequence of the human genome for Alu Yb-lineage subfamily members present on autosomal chromosomes. A total of 1,733 Yb Alu subfamily members have integrated into human autosomes. The average ages of Yb-lineage subfamilies, Yb7, Yb8 and Yb9, are estimated as 4.81, 2.39 and 2.32 million years, respectively. In order to determine the contribution of the Alu Yb-lineage to human genomic diversity, 1,202 loci were analysed using polymerase chain reaction (PCR-based assays, which amplify the genomic regions containing individual Yb-lineage subfamily members. Approximately 20 per cent of the Yb-lineage Alu elements are polymorphic for insertion presence/absence in the human genome. Fewer than 0.5 per cent of the Yb loci also demonstrate insertions at orthologous positions in non-human primate genomes. Genomic sequencing of these unusual loci demonstrates that each of the orthologous loci from non-human primate genomes contains older Y, Sg and Sx Alu family members that have been altered, through various mechanisms, into Yb8 sequences. These data suggest that Alu Yb-lineage subfamily members are largely restricted to the human genome. The high copy number, level of insertion polymorphism and estimated age indicate that members of the Alu Yb elements will be useful in a wide range of genetic analyses.

Six new genera of Braconidae (Hymenoptera) from China

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Achterberg, van C.; Chen, X.

2004-01-01

Six new genera of the family Braconidae (Hymenoptera) from China are described and illustrated: two genera of the subfamily Agathidinae: Facilagathis gen. nov. (type species: F. spinulata spec. nov.) and Cremnoptoides gen. nov. (type species: Cremnops pappi Sharkey, 1994); one genus of the subfamily

Rec8p, a meiotic recombination and sister chromatid cohesion phosphoprotein of the Rad21p family conserved from fision yeast to humans.

NARCIS (Netherlands)

S. Parisi; M.J. McKay (Michael); M. Molnar; M.A. Thompson (Anne); P.J. van der Spek (Peter); E. van Drunen-Schoenmaker; R. Kanaar (Roland); E. Lehmann; J.H.J. Hoeijmakers (Jan); J. Kohli

1999-01-01

textabstractOur work and that of others defined mitosis-specific (Rad21 subfamily) and meiosis-specific (Rec8 subfamily) proteins involved in sister chromatid cohesion in several eukaryotes, including humans. Mutation of the fission yeast Schizosaccharomyces pombe rec8 gene was previously shown to

Comparative ribotyping of Staphylococcus intermedius isolated from members of the Canoidea gives possible evidence for host-specificity and co-evolution of bacteria and hosts

DEFF Research Database (Denmark)

Aarestrup, Frank Møller

2001-01-01

A total of 41 Staphylococcus intermedius isolates were isolated from skin of healthy members of six phylogenetic groups within the Canoidea (the dog family, skunk subfamily, weasel subfamily, racoon family, red panda and bear family) of different geographical origin and compared by EcoRI ribotyping...

Conversion of the low affinity ouabain-binding site of non-gastric H,K-ATPase into a high affinity binding site by substitution of only five amino acids.

NARCIS (Netherlands)

Qiu, L.Y.; Swarts, H.G.P.; Tonk, E.C.; Willems, P.H.G.M.; Koenderink, J.B.; Pont, J.J.H.H.M. de

2006-01-01

P-type ATPases of the IIC subfamily exhibit large differences in sensitivity toward ouabain. This allows a strategy in which ouabain-insensitive members of this subfamily are used as template for mutational elucidation of the ouabain-binding site. With this strategy, we recently identified seven

Three-way interactions between Fusarium species, their plant hosts and biocontrol organisms

DEFF Research Database (Denmark)

Kosawang, Chatchai

of ABC transporters in mycoparasitic fungi focused on C. rosea and Trichoderma spp. We showed that expression of zhd101 depended on concentrations of ZEA and that the gene was not induced by other agents, suggesting specificity of the enzyme towards ZEA and its derivates. To investigate effects of ZEA...... identified expansion of ABC transporter families in C. rosea as in Trichoderma virens and T. harzianum, but not in T. reesei and T. atroviridae. The expansion was profoundly observed in the subfamily G of C. rosea ABC transporters and the subfamily C of Trichoderma spp, repectively. The subfamilies C and G...

Rare royal families in honeybees, Apis mellifera

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Moritz, Robin F. A.; Lattorff, H. Michael G.; Neumann, Peter; Kraus, F. Bernhard; Radloff, Sarah E.; Hepburn, H. Randall

2005-10-01

The queen is the dominant female in the honeybee colony, Apis mellifera, and controls reproduction. Queen larvae are selected by the workers and are fed a special diet (royal jelly), which determines caste. Because queens mate with many males a large number of subfamilies coexist in the colony. As a consequence, there is a considerable potential for conflict among the subfamilies over queen rearing. Here we show that honeybee queens are not reared at random but are preferentially reared from rare “royal” subfamilies, which have extremely low frequencies in the colony's worker force but a high frequency in the queens reared.

Revision of the Euagathis species (Hymenoptera: Braconidae: Bassinae) from the Sunda Islands

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Simbolotti, G.; Achterberg, van C.

1994-01-01

The species of the genus Euagathis Szépligeti, 1900 (Braconidae: Bassinae (= Agathidinae)) from the Greater and Lesser Sunda Islands (including West Malaysia) are revised and keyed. The subfamily name Bassinae Nees, 1812, is used because it is senior to the commonly used subfamily name Agathidinae

A perspective on the structural studies of inner membrane electrochemical potential-driven transporters.

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Lemieux, M Joanne

2008-09-01

Electrochemical potential-driven transporters represent a vast array of proteins with varied substrate specificities. While diverse in size and substrate specificity, they are all driven by electrochemical potentials. Over the past five years there have been increasing numbers of X-ray structures reported for this family of transporters. Structural information is available for five subfamilies of electrochemical potential-driven transporters. No structural information exists for the remaining 91 subfamilies. In this review, the various subfamilies of electrochemical potential-driven transporters are discussed. The seven reported structures for the electrochemical potential-driven transporters and the methods for their crystallization are also presented. With a few exceptions, overall crystallization trends have been very similar for the transporters despite their differences in substrate specificity and topology. Also discussed is why the structural studies on these transporters were successful while others are not as fruitful. With the plethora of transporters with unknown structures, this review provides incentive for crystallization of transporters in the remaining subfamilies for which no structural information exists.

Phylogenetic relationships of corallinaceae (Corallinales, Rhodophyta): taxonomic implications for reef-building corallines.

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Rösler, Anja; Perfectti, Francisco; Peña, Viviana; Braga, Juan Carlos

2016-06-01

A new, more complete, five-marker (SSU, LSU, psbA, COI, 23S) molecular phylogeny of the family Corallinaceae, order Corallinales, shows a paraphyletic grouping of seven well-supported monophyletic clades. The taxonomic implications included the amendment of two subfamilies, Neogoniolithoideae and Metagoniolithoideae, and the rejection of Porolithoideae as an independent subfamily. Metagoniolithoideae contained Harveylithon gen. nov., with H. rupestre comb. nov. as the generitype, and H. canariense stat. nov., H. munitum comb. nov., and H. samoënse comb. nov. Spongites and Pneophyllum belonged to separate clades. The subfamily Neogoniolithoideae included the generitype of Spongites, S. fruticulosus, for which an epitype was designated. Pneophyllum requires reassesment. The generitype of Hydrolithon, H. reinboldii, was a younger heterotypic synonym of H. boergesenii. The evolutionary novelty of the subfamilies Hydrolithoideae, Metagoniolithoideae, and Lithophylloideae was the development of tetra/bisporangial conceptacle roofs by filaments surrounding and interspersed among the sporangial initials. © 2016 Phycological Society of America.

Early evolution of the LIM homeobox gene family

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Srivastava, Mansi; Larroux, Claire; Lu, Daniel R; Mohanty, Kareshma; Chapman, Jarrod; Degnan, Bernard M; Rokhsar, Daniel S

2010-01-01

LIM homeobox (Lhx) transcription factors are unique to the animal lineage and have patterning roles during embryonic development in flies, nematodes and vertebrates, with a conserved role in specifying neuronal identity. Though genes of this family have been reported in a sponge and a cnidarian, the expression patterns and functions of the Lhx family during development in non-bilaterian phyla are not known. We identified Lhx genes in two cnidarians and a placozoan and report the expression of Lhx genes during embryonic development in Nematostella and the demosponge Amphimedon. Members of the six major LIM homeobox subfamilies are represented in the genomes of the starlet sea anemone, Nematostella vectensis, and the placozoan Trichoplax adhaerens. The hydrozoan cnidarian, Hydra magnipapillata, has retained four of the six Lhx subfamilies, but apparently lost two others. Only three subfamilies are represented in the haplosclerid demosponge Amphimedon queenslandica. A tandem cluster of three Lhx genes of different subfamilies and a gene containing two LIM domains in the genome of T. adhaerens (an animal without any neurons) indicates that Lhx subfamilies were generated by tandem duplication. This tandem cluster in Trichoplax is likely a remnant of the original chromosomal context in which Lhx subfamilies first appeared. Three of the six Trichoplax Lhx genes are expressed in animals in laboratory culture, as are all Lhx genes in Hydra. Expression patterns of Nematostella Lhx genes correlate with neural territories in larval and juvenile polyp stages. In the aneural demosponge, A. queenslandica, the three Lhx genes are expressed widely during development, including in cells that are associated with the larval photosensory ring. The Lhx family expanded and diversified early in animal evolution, with all six subfamilies already diverged prior to the cnidarian-placozoan-bilaterian last common ancestor. In Nematostella, Lhx gene expression is correlated with neural

Early evolution of the LIM homeobox gene family

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Degnan Bernard M

2010-01-01

Full Text Available Abstract Background LIM homeobox (Lhx transcription factors are unique to the animal lineage and have patterning roles during embryonic development in flies, nematodes and vertebrates, with a conserved role in specifying neuronal identity. Though genes of this family have been reported in a sponge and a cnidarian, the expression patterns and functions of the Lhx family during development in non-bilaterian phyla are not known. Results We identified Lhx genes in two cnidarians and a placozoan and report the expression of Lhx genes during embryonic development in Nematostella and the demosponge Amphimedon. Members of the six major LIM homeobox subfamilies are represented in the genomes of the starlet sea anemone, Nematostella vectensis, and the placozoan Trichoplax adhaerens. The hydrozoan cnidarian, Hydra magnipapillata, has retained four of the six Lhx subfamilies, but apparently lost two others. Only three subfamilies are represented in the haplosclerid demosponge Amphimedon queenslandica. A tandem cluster of three Lhx genes of different subfamilies and a gene containing two LIM domains in the genome of T. adhaerens (an animal without any neurons indicates that Lhx subfamilies were generated by tandem duplication. This tandem cluster in Trichoplax is likely a remnant of the original chromosomal context in which Lhx subfamilies first appeared. Three of the six Trichoplax Lhx genes are expressed in animals in laboratory culture, as are all Lhx genes in Hydra. Expression patterns of Nematostella Lhx genes correlate with neural territories in larval and juvenile polyp stages. In the aneural demosponge, A. queenslandica, the three Lhx genes are expressed widely during development, including in cells that are associated with the larval photosensory ring. Conclusions The Lhx family expanded and diversified early in animal evolution, with all six subfamilies already diverged prior to the cnidarian-placozoan-bilaterian last common ancestor. In

Catálogo de Tipulomorpha (Diptera: tipulidae-limoniidae de Venezuela, con el registro de Brachypremna spp., Gonomyia spp. y Dicranomyia spp. en el estado Falcón | Catalogue of Tipulomorpha (Diptera: tipulidae- limoniidae of Venezuela, with record of Brachypremna spp., Gonomyia spp. and Dicranomyia spp. in Falcón state

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Dalmiro Cazorla-Perfetti

2017-11-01

Full Text Available The infraorden Tipulomorpha contains insects of the order Diptera, suborder Nematocera commonly called as crane flies. Based on information from the Catalogue of the Crane flies of World, in the presente article a revised and updated checklist of the Tipulomorpha (superfamily Tipuloidea registered from Venezuela is shown. Until now, 226 valid species of crane flies has been recorded, grouped into two families, 5 subfamilies and 40 genera, including family Tipulidae s.s., subfamily Tipulinae (genera Brachypremna: 6 species; Leptotarsus: 8 species; Nephrotoma: 3 species; Ozodicera: 3 species; Tipula: 28 species; Zelandotipula: 6 species and the subfamily Ctenophorinae (genus Pselliophora: 1 species; family Limoniidae, subfamily Chioneinae (genera Atarba: 6 species; Cheilotrichia: 1 species; Cryptolabis: 1 species; Ellipteroides: 2 species; Erioptera: 3 species; Eriopterodes: 1 species; Eugnophomyia: 1 species; Gnophomyia: 4 species; Gonomyia: 9 species; Molophilus: 5 species; Neognophomyia: 1 species; Rhabdomastix: 1 species; Sigmatomera: 1 species; Styringomyia: 1 species; Teucholabis: 15 species; subfamily Limnophilinae (genera Austrolimnophila: 1 species; Epiphragma: 10 species; Hexatoma: 11 species; Lecteria: 1 species; Limnophila: 5 species; Paradelphomyia: 1 species; Polymera: 3 species; Shannonomyia: 5 species;; and subfamily Limoniinae (Dicranomyia: 26 species; Elephantomyia: 1 species; Geranomyia: 25 species; Helius: 5 species; Neolimonia: 2 species; Orimarga: 4 species; Protohelius: 1 species; Rhipidia: 10 species; Toxorhina: 4 species; Trentepohlia: 4 species. In addition, the first records of Brachypremna spp., Gonomyia spp. and Dicranomyia spp. are described for the urban semiarid area from Falcon state, north-western region. Data on the geographical distribution of the species is provided, and bio-ecological, agronomic, medical relevance and research needs on the Venezuelan crane flies, are discussed.

The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots

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Zhitao Niu

2017-05-01

Full Text Available Orchidaceae (orchids is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented. In this study, we compared 53 orchid plastomes, including four newly sequenced ones, that represent four remote genera: Dendrobium, Goodyera, Paphiopedilum, and Vanilla. These differ from one another not only in their lengths of inverted repeats and small single copy regions but also in their retention of ndh genes. Comparative analyses of the plastomes revealed that the expansion of inverted repeats in Paphiopedilum and Vanilla is associated with a loss of ndh genes. In orchid plastomes, mutational hotspots are genus specific. After having carefully examined the data, we propose that the three loci 5′trnK-rps16, trnS-trnG, and rps16-trnQ might be powerful markers for genera within Epidendroideae, and clpP-psbB and rps16-trnQ might be markers for genera within Cypripedioideae. After analyses of a partitioned dataset, we found that our plastid phylogenomic trees were congruent in a topology where two one-stamened subfamilies (i.e., Epidendroideae and Orchidoideae were sisters to a multi-stamened subfamily (i.e., Cypripedioideae rather than to the other one-stamened subfamily (Vanilloideae, suggesting that the living one-stamened orchids are paraphyletic.

FAMILY CHIRONOMIDAE.

Science.gov (United States)

Mendes, Humberto Fonseca; Pinho, Luiz Carlos

2016-06-14

Only 30 chironomid species distributed in 16 genera and three subfamilies are formally recorded to Colombia. Another 32 genera and two subfamilies have been recorded on larval stage, with no identification at species level. Many new records, genera and species are expected when focusing on systematics of chironomids from Colombia.

Barley HvHMA1 is a heavy metal pump involved in mobilizing organellar Zn and Cu and plays a role in metal loading into grains

DEFF Research Database (Denmark)

Mikkelsen, Maria Dalgaard; Pedas, Pai; Schiller, Michaela

2012-01-01

Heavy metal transporters belonging to the P1B-ATPase subfamily of P-type ATPases are key players in cellular heavy metal homeostasis. Heavy metal transporters belonging to the P1B-ATPase subfamily of P-type ATPases are key players in cellular heavy metal homeostasis. In this study we investigated...

Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae

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de Stephanis Renaud

2011-03-01

Full Text Available Abstract Background Previous DNA-based phylogenetic studies of the Delphinidae family suggest it has undergone rapid diversification, as characterised by unresolved and poorly supported taxonomic relationships (polytomies for some of the species within this group. Using an increased amount of sequence data we test between alternative hypotheses of soft polytomies caused by rapid speciation, slow evolutionary rate and/or insufficient sequence data, and hard polytomies caused by simultaneous speciation within this family. Combining the mitogenome sequences of five new and 12 previously published species within the Delphinidae, we used Bayesian and maximum-likelihood methods to estimate the phylogeny from partitioned and unpartitioned mitogenome sequences. Further ad hoc tests were then conducted to estimate the support for alternative topologies. Results We found high support for all the relationships within our reconstructed phylogenies, and topologies were consistent between the Bayesian and maximum-likelihood trees inferred from partitioned and unpartitioned data. Resolved relationships included the placement of the killer whale (Orcinus orca as sister taxon to the rest of the Globicephalinae subfamily, placement of the Risso's dolphin (Grampus griseus within the Globicephalinae subfamily, removal of the white-beaked dolphin (Lagenorhynchus albirostris from the Delphininae subfamily and the placement of the rough-toothed dolphin (Steno bredanensis as sister taxon to the rest of the Delphininae subfamily rather than within the Globicephalinae subfamily. The additional testing of alternative topologies allowed us to reject all other putative relationships, with the exception that we were unable to reject the hypothesis that the relationship between L. albirostris and the Globicephalinae and Delphininae subfamilies was polytomic. Conclusion Despite their rapid diversification, the increased sequence data yielded by mitogenomes enables the

Hybrid and rogue kinases encoded in the genomes of model eukaryotes.

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Ramaswamy Rakshambikai

Full Text Available The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes-S.cerevisiae, D. melanogaster, C.elegans, M.musculus, T.rubripes and H.sapiens-and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P.falciparum sheds light on possible strategies in host-pathogen interactions.

IL17 factors are early regulators in the gut epithelium during inflammatory response to Vibrio in the sea urchin larva

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Buckley, Katherine M; Ho, Eric Chun Hei; Hibino, Taku; Schrankel, Catherine S; Schuh, Nicholas W; Wang, Guizhi; Rast, Jonathan P

2017-01-01

IL17 cytokines are central mediators of mammalian immunity. In vertebrates, these factors derive from diverse cellular sources. Sea urchins share a molecular heritage with chordates that includes the IL17 system. Here, we characterize the role of epithelial expression of IL17 in the larval gut-associated immune response. The purple sea urchin genome encodes 10 IL17 subfamilies (35 genes) and 2 IL17 receptors. Most of these subfamilies are conserved throughout echinoderms. Two IL17 subfamilies are sequentially strongly upregulated and attenuated in the gut epithelium in response to bacterial disturbance. IL17R1 signal perturbation results in reduced expression of several response genes including an IL17 subtype, indicating a potential feedback. A third IL17 subfamily is activated in adult immune cells indicating that expression in immune cells and epithelia is divided among families. The larva provides a tractable model to investigate the regulation and consequences of gut epithelial IL17 expression across the organism. DOI: http://dx.doi.org/10.7554/eLife.23481.001 PMID:28447937

Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy.

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Xia, Rong; Durand, Jean-Dominique; Fu, Cuizhang

2016-03-01

The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera. Copyright © 2015 Elsevier Inc. All rights reserved.

Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in the silkworm, Bombyx mori.

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Xie, Xiaodong; Cheng, Tingcai; Wang, Genhong; Duan, Jun; Niu, Weihuan; Xia, Qingyou

2012-07-01

The ATP-binding cassette (ABC) superfamily is a larger protein family with diverse physiological functions in all kingdoms of life. We identified 53 ABC transporters in the silkworm genome, and classified them into eight subfamilies (A-H). Comparative genome analysis revealed that the silkworm has an expanded ABCC subfamily with more members than Drosophila melanogaster, Caenorhabditis elegans, or Homo sapiens. Phylogenetic analysis showed that the ABCE and ABCF genes were highly conserved in the silkworm, indicating possible involvement in fundamental biological processes. Five multidrug resistance-related genes in the ABCB subfamily and two multidrug resistance-associated-related genes in the ABCC subfamily indicated involvement in biochemical defense. Genetic variation analysis revealed four ABC genes that might be evolving under positive selection. Moreover, the silkworm ABCC4 gene might be important for silkworm domestication. Microarray analysis showed that the silkworm ABC genes had distinct expression patterns in different tissues on day 3 of the fifth instar. These results might provide new insights for further functional studies on the ABC genes in the silkworm genome.

THE ASIATIC SPECIES OF LINDENBERGIA Lehm. (Scrophulariaceae

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B. PRIJANTO*

1969-03-01

Full Text Available Lindenbergia is represented in Asia by 7 species. Based on the hairiness oftheir ovaries L. muraria (Roxb. Briihl (= L. urticifolia Lehm. and L. indica(L. Vatke (= L. polyantha Benth. are reinstated as distinct species. I followBentham in including Lindenbergia in the tribe Gratioleae.Objection to the use of the aestivation of corolla as the only positivecharacter for distinguishing subfamilies of the Scrophulariaceae is put forward;it is shown that several genera (Lindenbergia, Isoplexis, Lagotis, Erinus, Frey-linia,, Phygelius and Mimulus considered to belong to one subfamily actuallyhave the aestivation character of the other subfamily.The occurrence of resupinatton of the flower in Dopatrium juncewm (Roxb.Buch.-Ham. ex Benth. is recorded for the first time.

Morphology of the axial skeleton of seven bat genera (Chiroptera: Phyllostomidae

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PABLO J. GAUDIOSO

2017-10-01

Full Text Available ABSTRACT Here we present detailed descriptions and comparisons of the axial skeleton of seven species of bats belonging to five subfamilies of Phyllostomidae of different trophic guilds. The material examined consisted of 34 complete skeletons of seven species. For five of the studied species, previous descriptions have not been conducted, and for the vampires only limited information is available, so that descriptions for these species are here completed. The axial skeleton has characters that allow grouping of the species phylogenetically of the same subfamily and by feeding habits. At the same time, there are characters that associate species from different subfamilies with different types of diet or ways to obtain food.

Cytochrome P450 CYP3A in marsupials: cloning and identification of the first CYP3A subfamily member, isoform 3A70 from Eastern gray kangaroo (Macropus giganteus).

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El-Merhibi, Adaweyah; Ngo, Suong N T; Marchant, Ceilidh L; Height, Tamara A; Stupans, Ieva; McKinnon, Ross A

2012-09-15

Australian marsupials are unique fauna that have evolved and adapted to unique environments and thus it is likely that their detoxification systems differ considerably from those of well-studied eutherian mammals. Knowledge of these processes in marsupials is therefore vital to understanding the consequences of exposure to xenobiotics. Cytochromes P450 (CYPs) are critically important in the oxidative metabolism of a diverse array of both xenobiotics and endogenous substrates. In this study we have cloned and characterized CYP3A70, the first identified member of the CYP3A gene subfamily from Eastern gray kangaroo (Macropus giganteus). A 1665 base pair kangaroo hepatic CYP3A complete cDNA, designated CYP3A70, was cloned by reverse transcription-polymerase chain reaction approaches, which encodes a protein of 506 amino acids. The CYP3A70 cDNA shares approximately 71% nucleotide and 65% amino acid sequence homology to human CYP3A4 and displays high sequence similarity to other published mammalian CYP3As from human, monkey, cow, pig, dog, rat, rabbit, mouse, hamster, and guinea pig. Transfection of the CYP3A70 cDNAs into 293T cells resulted in stable cell lines expressing a CYP3A immuno-reactive protein that was recognized by a goat anti-human CYP3A4 polyclonal antibody. The anti-human CYP3A4 antibody also detected immunoreactive proteins in liver microsomes from all test marsupials, including the kangaroo, koala, wallaby, and wombat, with multiple CYP3A immunoreactive bands observed in kangaroo and wallaby tissues. Relatively, very low CYP catalytic activity was detected for the kangaroo CYP3A70 cDNA-expressed proteins (19.6 relative luminescent units/μg protein), which may be due to low protein expression levels. Collectively, this study provides primary molecular data regarding the Eastern kangaroo hepatic CYP3A70 gene and enables further functional analyses of CYP3A enzymes in marsupials. Copyright © 2012 Elsevier B.V. All rights reserved.

NCBI nr-aa BLAST: CBRC-TGUT-08-0001 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-TGUT-08-0001 ref|NP_067250.2| potassium voltage-gated channel, shaker-related ...assium voltage-gated channel, shaker-related subfamily, member 4 [Mus musculus] emb|CAM23761.1| potassium voltage-gated channel, shak...4.1| potassium voltage-gated channel, shaker-related subfamily, member 4 [Mus musculus] NP_067250.2 0.0 79% ...

NCBI nr-aa BLAST: CBRC-ACAR-01-0365 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-ACAR-01-0365 ref|NP_067250.2| potassium voltage-gated channel, shaker-related ...assium voltage-gated channel, shaker-related subfamily, member 4 [Mus musculus] emb|CAM23761.1| potassium voltage-gated channel, shak...4.1| potassium voltage-gated channel, shaker-related subfamily, member 4 [Mus musculus] NP_067250.2 0.0 79% ...

NCBI nr-aa BLAST: CBRC-MLUC-01-0737 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-MLUC-01-0737 ref|NP_067250.2| potassium voltage-gated channel, shaker-related ...assium voltage-gated channel, shaker-related subfamily, member 4 [Mus musculus] emb|CAM23761.1| potassium voltage-gated channel, shak...4.1| potassium voltage-gated channel, shaker-related subfamily, member 4 [Mus musculus] NP_067250.2 0.0 87% ...

NCBI nr-aa BLAST: CBRC-ETEL-01-1362 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-ETEL-01-1362 ref|NP_067250.2| potassium voltage-gated channel, shaker-related ...assium voltage-gated channel, shaker-related subfamily, member 4 [Mus musculus] emb|CAM23761.1| potassium voltage-gated channel, shak...4.1| potassium voltage-gated channel, shaker-related subfamily, member 4 [Mus musculus] NP_067250.2 0.0 93% ...

NCBI nr-aa BLAST: CBRC-OANA-01-2250 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-OANA-01-2250 ref|NP_067250.2| potassium voltage-gated channel, shaker-related ...assium voltage-gated channel, shaker-related subfamily, member 4 [Mus musculus] emb|CAM23761.1| potassium voltage-gated channel, shak...4.1| potassium voltage-gated channel, shaker-related subfamily, member 4 [Mus musculus] NP_067250.2 0.0 92% ...

Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in sea lamprey and Japanese lamprey.

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Ren, Jianfeng; Chung-Davidson, Yu-Wen; Yeh, Chu-Yin; Scott, Camille; Brown, Titus; Li, Weiming

2015-06-06

Lampreys are extant representatives of the jawless vertebrate lineage that diverged from jawed vertebrates around 500 million years ago. Lamprey genomes contain information crucial for understanding the evolution of gene families in vertebrates. The ATP-binding cassette (ABC) gene family is found from prokaryotes to eukaryotes. The recent availability of two lamprey draft genomes from sea lamprey Petromyzon marinus and Japanese lamprey Lethenteron japonicum presents an opportunity to infer early evolutionary events of ABC genes in vertebrates. We conducted a genome-wide survey of the ABC gene family in two lamprey draft genomes. A total of 37 ABC transporters were identified and classified into seven subfamilies; namely seven ABCA genes, 10 ABCB genes, 10 ABCC genes, three ABCD genes, one ABCE gene, three ABCF genes, and three ABCG genes. The ABCA subfamily has expanded from three genes in sea squirts, seven and nine in lampreys and zebrafish, to 13 and 16 in human and mouse. Conversely, the multiple copies of ABCB1-, ABCG1-, and ABCG2-like genes found in sea squirts have contracted in the other species examined. ABCB2 and ABCB3 seem to be new additions in gnathostomes (not in sea squirts or lampreys), which coincides with the emergence of the gnathostome-specific adaptive immune system. All the genes in the ABCD, ABCE and ABCF subfamilies were conserved and had undergone limited duplication and loss events. In the sea lamprey transcriptomes, the ABCE and ABCF gene subfamilies were ubiquitously and highly expressed in all tissues while the members in other gene subfamilies were differentially expressed. Thirteen more lamprey ABC transporter genes were identified in this study compared with a previous study. By concatenating the same gene sequences from the two lampreys, more full length sequences were obtained, which significantly improved both the assignment of gene names and the phylogenetic trees compared with a previous analysis using partial sequences. The ABC

Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm

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Xiaoli Jin

2017-06-01

Full Text Available NAC (NAM/ATAF/CUC proteins constitute one of the biggest plant-specific transcription factor (TF families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1 uneven constitution of Clusters of Orthologous Groups (COGs and contrasting birth/death rates among subfamilies, and (2 two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses.

Survey of familial glaucoma shows a high incidence of cytochrome P450, family 1, subfamily B, polypeptide 1 (CYP1B1) mutations in non-consanguineous congenital forms in a Spanish population

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Millá, Elena; Mañé, Begoña; Duch, Susana; Hernan, Imma; Borràs, Emma; Planas, Ester; Dias, Miguel de Sousa; Carballo, Miguel

2013-01-01

Purpose To identify myocilin (MYOC) and cytochrome P450, family 1, subfamily B, polypeptide 1 (CYP1B1) mutations in a Spanish population with different clinical forms of familial glaucoma or ocular hypertension (OHT). Methods Index patients from 226 families participated in this study. Patients were diagnosed with familial glaucoma or OHT by complete ophthalmologic examination. Screening for MYOC mutations was performed in 207 index patients: 96 with adult-onset primary open-angle glaucoma (POAG), 21 with primary congenital glaucoma (PCG), 18 with juvenile-onset open-angle glaucoma (JOAG), five with Axenfeld-Rieger syndrome (ARS), and 67 with other types of glaucoma. One hundred two of the families (including all those in whom a MYOC mutation was detected) were also screened for CYP1B1 mutations: 45 POAG, 25 PCG, 21 JOAG, four ARS, and seven others. Results We examined 292 individuals (patients and relatives) with a positive family history of glaucoma or OHT. We identified two novel MYOC variants, p.Lys39Arg and p.Glu218Lys, in two families with POAG, and six previously reported MYOC mutations in seven families with POAG (four), JOAG (one), PCG (one), and normotensive glaucoma (one). CYP1B1 mutations were found in 16 index patients with PCG (nine), POAG (three), JOAG (two), and ARS (two). Conclusions The high percentage (9/25=36%) of mutations in CYP1B1 found in non-consanguineous patients with congenital glaucoma mandates genetic testing. However, the percentage of mutations (9/207=4.4%) in MYOC associated with glaucoma is relatively low in our population. The variable phenotype expression of glaucoma, even in families, cannot be explained with a digenic mechanism between MYOC and CYP1B1. PMID:23922489

PEA3/ETV4-related transcription factors coupled with active ERK signalling are associated with poor prognosis in gastric adenocarcinoma

LENUS (Irish Health Repository)

Keld, R

2011-06-28

Background: Transcription factors often play important roles in tumourigenesis. Members of the PEA3 subfamily of ETS-domain transcription factors fulfil such a role and have been associated with tumour metastasis in several different cancers. Moreover, the activity of the PEA3 subfamily transcription factors is potentiated by Ras-ERK pathway signalling, which is itself often deregulated in tumour cells.\\r\

Revision of the subfamily Opiinae (Hymenoptera, Braconidae from Hunan (China, including thirty-six new species and two new genera

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Li Xi-Ying

2013-02-01

Full Text Available The species of the subfamily Opiinae (Hymenoptera: Braconidae from Hunan (Oriental China are revised and illustrated. Thirty-six new species are described: Apodesmia bruniclypealis Li & van Achterberg, sp. n., A. melliclypealis Li & van Achterberg, sp. n., Areotetes albiferus Li & van Achterberg, sp. n., Areotetes carinuliferus Li & van Achterberg, sp. n., A. striatiferus Li & van Achterberg, sp. n., Coleopioides diversinotum Li & van Achterberg, sp. n., C. postpectalis Li & van Achterberg, sp. n., Fopius dorsopiferus Li, van Achterberg & Tan, sp. n., Indiopius chenae Li & van Achterberg, sp. n., Opiognathus aulaciferus Li & van Achterberg, sp. n., O. brevibasalis Li & van Achterberg, sp. n., Opius crenuliferus Li & van Achterberg, sp. n., O. malarator Li, van Achterberg & Tan, sp. n., O. monilipalpis Li & van Achterberg, sp. n., O. pachymerus Li & van Achterberg, sp. n., O. songi Li & van Achterberg, sp. n., O. youi Li & van Achterberg, sp. n., O. zengi Li & van Achterberg, sp. n., Phaedrotoma acuticlypeata Li & van Achterberg, sp. n., P.angiclypeata Li & van Achterberg, sp. n., P. antenervalis Li & van Achterberg, sp. n., P. depressiclypealis Li & van Achterberg, sp. n., P. flavisoma Li & van Achterberg, sp. n., P. nigrisoma Li & van Achterberg, sp. n., P. protuberator Li & van Achterberg, sp. n., P. rugulifera Li & van Achterberg, sp. n., Li & van Achterberg, P. striatinota Li & van Achterberg, sp. n., P. vermiculifera Li & van Achterberg, sp. n., Rhogadopsis latipennis Li & van Achterberg, sp. n., R. longicaudifera Li & van Achterberg, sp. n., R. maculosa Li, van Achterberg & Tan, sp. n., R. obliqua Li & van Achterberg, sp. n., R. sculpturator Li & van Achterberg, sp. n., Utetes longicarinatus Li & van Achterberg, sp. n. and Xynobius notauliferus Li & van Achterberg, sp. n. Areotetes van Achterberg & Li, gen. n. (type species: Areotetes carinuliferus sp. n. and Coleopioides van Achterberg & Li, gen. n. (type species: Coleopioides

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae).

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Yang, Chien-Hui; Bracken-Grissom, Heather; Kim, Dohyup; Crandall, Keith A; Chan, Tin-Yam

2012-01-01

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification. Copyright © 2011 Elsevier Inc. All rights reserved.

BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea.

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Zhang, Xiaoyu; Wessler, Susan R

2005-05-01

Short interspersed elements (SINEs) are nonautonomous non-LTR retrotransposons that populate eukaryotic genomes. Numerous SINE families have been identified in animals, whereas only a few have been described in plants. Here we describe a new family of SINEs, named BoS, that is widespread in Brassicaceae and present at approximately 2000 copies in Brassica oleracea. In addition to sharing a modular structure and target site preference with previously described SINEs, BoS elements have several unusual features. First, the head regions of BoS RNAs can adopt a distinct hairpin-like secondary structure. Second, with 15 distinct subfamilies, BoS represents one of the most diverse SINE families described to date. Third, several of the subfamilies have a mosaic structure that has arisen through the exchange of sequences between existing subfamilies, possibly during retrotransposition. Analysis of BoS subfamilies indicate that they were active during various time periods through the evolution of Brassicaceae and that active elements may still reside in some Brassica species. As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family.

Functional Analyses of Resurrected and Contemporary Enzymes Illuminate an Evolutionary Path for the Emergence of Exolysis in Polysaccharide Lyase Family 2.

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McLean, Richard; Hobbs, Joanne K; Suits, Michael D; Tuomivaara, Sami T; Jones, Darryl R; Boraston, Alisdair B; Abbott, D Wade

2015-08-28

Family 2 polysaccharide lyases (PL2s) preferentially catalyze the β-elimination of homogalacturonan using transition metals as catalytic cofactors. PL2 is divided into two subfamilies that have been generally associated with secretion, Mg(2+) dependence, and endolysis (subfamily 1) and with intracellular localization, Mn(2+) dependence, and exolysis (subfamily 2). When present within a genome, PL2 genes are typically found as tandem copies, which suggests that they provide complementary activities at different stages along a catabolic cascade. This relationship most likely evolved by gene duplication and functional divergence (i.e. neofunctionalization). Although the molecular basis of subfamily 1 endolytic activity is understood, the adaptations within the active site of subfamily 2 enzymes that contribute to exolysis have not been determined. In order to investigate this relationship, we have conducted a comparative enzymatic analysis of enzymes dispersed within the PL2 phylogenetic tree and elucidated the structure of VvPL2 from Vibrio vulnificus YJ016, which represents a transitional member between subfamiles 1 and 2. In addition, we have used ancestral sequence reconstruction to functionally investigate the segregated evolutionary history of PL2 progenitor enzymes and illuminate the molecular evolution of exolysis. This study highlights that ancestral sequence reconstruction in combination with the comparative analysis of contemporary and resurrected enzymes holds promise for elucidating the origins and activities of other carbohydrate active enzyme families and the biological significance of cryptic metabolic pathways, such as pectinolysis within the zoonotic marine pathogen V. vulnificus. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Identification and genomic characterization of a novel porcine parvovirus (PPV6) in China.

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Ni, Jianqiang; Qiao, Caixia; Han, Xue; Han, Tao; Kang, Wenhua; Zi, Zhanchao; Cao, Zhen; Zhai, Xinyan; Cai, Xuepeng

2014-12-02

Parvoviruses are classified into two subfamilies based on their host range: the Parvovirinae, which infect vertebrates, and the Densovirinae, which mainly infect insects and other arthropods. In recent years, a number of novel parvoviruses belonging to the subfamily Parvovirinae have been identified from various animal species and humans, including human parvovirus 4 (PARV4), porcine hokovirus, ovine partetravirus, porcine parvovirus 4 (PPV4), and porcine parvovirus 5 (PPV5). Using sequence-independent single primer amplification (SISPA), a novel parvovirus within the subfamily Parvovirinae that was distinct from any known parvoviruses was identified and five full-length genome sequences were determined and analyzed. A novel porcine parvovirus, provisionally named PPV6, was initially identified from aborted pig fetuses in China. Retrospective studies revealed the prevalence of PPV6 in aborted pig fetuses and piglets(50% and 75%, respectively) was apparently higher than that in finishing pigs and sows (15.6% and 3.8% respectively). Furthermore, the prevalence of PPV6 in finishing pig was similar in affected and unaffected farms (i.e. 16.7% vs. 13.6%-21.7%). This finding indicates that animal age, perhaps due to increased innate immune resistance, strongly influences the level of PPV6 viremia. Complete genome sequencing and multiple alignments have shown that the nearly full-length genome sequences were approximately 6,100 nucleotides in length and shared 20.5%-42.6% DNA sequence identity with other members of the Parvovirinae subfamily. Phylogenetic analysis showed that PPV6 was significantly distinct from other known parvoviruses and was most closely related to PPV4. Our findings and review of published parvovirus sequences suggested that a novel porcine parvovirus is currently circulating in China and might be classified into the novel genus Copiparvovirus within the subfamily Parvovirinae. However, the clinical manifestations of PPV6 are still unknown in that the

Molecular Characterization, Evolution, and Expression Profiling of the Dirigent (DIR Family Genes in Chinese White Pear (Pyrus bretschneideri

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Xi Cheng

2018-04-01

Full Text Available Stone cells content and size are the key factors determining the internal quality of the pear fruit. Synthesis of lignin and thickening of secondary cell wall are the keys to the development of stone cells. The polymerization of monolignols and secondary cell wall formation requires the participation of dirigent proteins (DIRs. In recent years, DIR family have been studied in higher plants, but lack of comprehensive study in the pear DIR (PbDIR family. This study focuses on the identification and analysis of PbDIR family for the first time. We identified 35 PbDIRs from the pear genome, 89% of which are intronless genes. Phylogenetic tree and chromosome localization analysis showed that 35 PbDIRs were divided into four subfamilies (DIR-a, -b/d, -e, and -g and irregularly distributed among 10 chromosomes. In addition, we identified 29, 26, and 14 DIRs from the other three Rosids (peach, Mei, and grape, respectively. Interspecies microsynteny analysis revealed the collinear gene pairs between pear and peach are the most. Temporal expression analysis showed that the expression changes of seven PbDIRs (DIR-a subfamily: PbDIR4 and PbDIR5; DIR-b/d subfamily: PbDIR11; DIR-g subfamily: PbDIR19; DIR-e subfamily: PbDIR23, 25 and 26 in fruits were consistent with the changes of fruit lignin and stone cells contents. In addition, the subfamily of PbDIRs in fruits showed significant responses after treatment with ABA, SA, and MeJA. According to the protein tertiary structure, key amino acid residues and expression patterns analysis found that PbDIR4 might be involved in the metabolism of lignin and related to stone cells contents in pear fruits. In this study, we systematically analyzed the structure, evolution, function and expression of PbDIR family, which not only confirmed the characteristics of PbDIR family, but also laid the foundation for revealing the role of DIR in pear stone cell development and lignin polymerization.

Susceptibility to invasive meningococcal disease: polymorphism of complement system genes and Neisseria meningitidis factor H binding protein.

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Declan T Bradley

Full Text Available Neisseria meningitidis can cause severe infection in humans. Polymorphism of Complement Factor H (CFH is associated with altered risk of invasive meningococcal disease (IMD. We aimed to find whether polymorphism of other complement genes altered risk and whether variation of N. meningitidis factor H binding protein (fHBP affected the risk association.We undertook a case-control study with 309 European cases and 5,200 1958 Birth Cohort and National Blood Service cohort controls. We used additive model logistic regression, accepting P<0.05 as significant after correction for multiple testing. The effects of fHBP subfamily on the age at infection and severity of disease was tested using the independent samples median test and Student's T test. The effect of CFH polymorphism on the N. meningitidis fHBP subfamily was investigated by logistic regression and Chi squared test.Rs12085435 A in C8B was associated with odds ratio (OR of IMD (0.35 [95% CI 0.19-0.67]; P = 0.03 after correction. A CFH haplotype tagged by rs3753396 G was associated with IMD (OR 0.56 [95% CI 0.42-0.76], P = 1.6x10⁻⁴. There was no bacterial load (CtrA cycle threshold difference associated with carriage of this haplotype. Host CFH haplotype and meningococcal fHBP subfamily were not associated. Individuals infected with meningococci expressing subfamily A fHBP were younger than those with subfamily B fHBP meningococci (median 1 vs 2 years; P = 0.025.The protective CFH haplotype alters odds of IMD without affecting bacterial load for affected heterozygotes. CFH haplotype did not affect the likelihood of infecting meningococci having either fHBP subfamily. The association between C8B rs12085435 and IMD requires independent replication. The CFH association is of interest because it is independent of known functional polymorphisms in CFH. As fHBP-containing vaccines are now in use, relationships between CFH polymorphism and vaccine effectiveness and side-effects may become

Analgesia and Opioids: A Pharmacogenetics Shortlist for Implementation in Clinical Practice.

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Matic, Maja; de Wildt, Saskia N; Tibboel, Dick; van Schaik, Ron H N

2017-07-01

The use of opioids to alleviate pain is complicated by the risk of severe adverse events and the large variability in dose requirements. Pharmacogenetics (PGx) could possibly be used to tailor pain medication based on an individual's genetic background. Many potential genetic markers have been described, and the importance of genetic predisposition in opioid efficacy and toxicity has been demonstrated in knockout mouse models and human twin studies. Such predictors are especially of value for neonates and young children, in whom the assessment of efficacy or side effects is complicated by the inability of the patient to communicate this properly. The current problem is determining which of the many potential candidates to focus on for clinical implementation. We systematically searched publications on PGx for opioids in 5 databases, aiming to identify PGx markers with sufficient robust data and high enough occurrence for potential clinical application. The initial search yielded 4257 unique citations, eventually resulting in 852 relevant articles covering 24 genes. From these genes, we evaluated the evidence and selected the most promising 10 markers: cytochrome P450 family 2 subfamily D member 6 ( CYP2D6 ), cytochrome P450 family 3 subfamily A member 4 ( CYP3A4 ), cytochrome P450 family 3 subfamily A member 5 ( CYP3A5 ), UDP glucuronosyltransferase family 2 member B7 ( UGT2B7 ), ATP binding cassette subfamily B member 1 ( ABCB1 ), ATP binding cassette subfamily C member 3 ( ABCC3 ), solute carrier family 22 member 1 ( SLC22A1 ), opioid receptor kappa 1 ( OPRM1 ), catechol- O -methyltransferase ( COMT ), and potassium voltage-gated channel subfamily J member 6 ( KCNJ6 ). Treatment guidelines based on genotype are already available only for CYP2D6 . The application of PGx in the management of pain with opioids has the potential to improve therapy. We provide a shortlist of 10 genes that are the most promising markers for clinical use in this context. © 2016

Using random forests for assistance in the curation of G-protein coupled receptor databases.

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Shkurin, Aleksei; Vellido, Alfredo

2017-08-18

Biology is experiencing a gradual but fast transformation from a laboratory-centred science towards a data-centred one. As such, it requires robust data engineering and the use of quantitative data analysis methods as part of database curation. This paper focuses on G protein-coupled receptors, a large and heterogeneous super-family of cell membrane proteins of interest to biology in general. One of its families, Class C, is of particular interest to pharmacology and drug design. This family is quite heterogeneous on its own, and the discrimination of its several sub-families is a challenging problem. In the absence of known crystal structure, such discrimination must rely on their primary amino acid sequences. We are interested not as much in achieving maximum sub-family discrimination accuracy using quantitative methods, but in exploring sequence misclassification behavior. Specifically, we are interested in isolating those sequences showing consistent misclassification, that is, sequences that are very often misclassified and almost always to the same wrong sub-family. Random forests are used for this analysis due to their ensemble nature, which makes them naturally suited to gauge the consistency of misclassification. This consistency is here defined through the voting scheme of their base tree classifiers. Detailed consistency results for the random forest ensemble classification were obtained for all receptors and for all data transformations of their unaligned primary sequences. Shortlists of the most consistently misclassified receptors for each subfamily and transformation, as well as an overall shortlist including those cases that were consistently misclassified across transformations, were obtained. The latter should be referred to experts for further investigation as a data curation task. The automatic discrimination of the Class C sub-families of G protein-coupled receptors from their unaligned primary sequences shows clear limits. This study has

Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes.

Science.gov (United States)

Sun, Jiangmei; Li, Leiting; Wang, Peng; Zhang, Shaoling; Wu, Juyou

2017-10-10

Leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants. However, the patterns of LRR-RLK gene family evolution in the five main Rosaceae species for which genome sequences are available have not yet been reported. In this study, we performed a comprehensive analysis of LRR-RLK genes for five Rosaceae species: Fragaria vesca (strawberry), Malus domestica (apple), Pyrus bretschneideri (Chinese white pear), Prunus mume (mei), and Prunus persica (peach), which contained 201, 244, 427, 267, and 258 LRR-RLK genes, respectively. All LRR-RLK genes were further grouped into 23 subfamilies based on the hidden Markov models approach. RLK-Pelle_LRR-XII-1, RLK-Pelle_LRR-XI-1, and RLK-Pelle_LRR-III were the three largest subfamilies. Synteny analysis indicated that there were 236 tandem duplicated genes in the five Rosaceae species, among which subfamilies XII-1 (82 genes) and XI-1 (80 genes) comprised 68.6%. Our results indicate that tandem duplication made a large contribution to the expansion of the subfamilies. The gene expression, tissue-specific expression, and subcellular localization data revealed that LRR-RLK genes were differentially expressed in various organs and tissues, and the largest subfamily XI-1 was highly expressed in all five Rosaceae species, suggesting that LRR-RLKs play important roles in each stage of plant growth and development. Taken together, our results provide an overview of the LRR-RLK family in Rosaceae genomes and the basis for further functional studies.

Genome-wide identification and characterization of odorant-binding protein (OBP) genes in the malaria vector Anopheles sinensis (Diptera: Culicidae).

Science.gov (United States)

He, Xiu; He, Zheng-Bo; Zhang, Yu-Juan; Zhou, Yong; Xian, Peng-Jie; Qiao, Liang; Chen, Bin

2016-06-01

Anopheles sinensis is a major malaria vector. Insect odorant-binding proteins (OBPs) may function in the reception of odorants in the olfactory system. The classification and characterization of the An. sinensis OBP genes have not been systematically studied. In this study, 64 putative OBP genes were identified at the whole-genome level of An. sinensis based on the comparison between OBP conserved motifs, PBP_GOBP, and phylogenetic analysis with An. gambiae OBPs. The characterization of An. sinensis OBPs, including the motif's conservation, gene structure, genomic organization and classification, were investigated. A new gene, AsOBP73, belonging to the Plus-C subfamily, was identified with the support of transcript and conservative motifs. These An. sinensis OBP genes were classified into three subfamilies with 37, 15 and 12 genes in the subfamily Classic, Atypical and Plus-C, respectively. The genomic organization of An. sinensis OBPs suggests a clustered distribution across nine different scaffolds. Eight genes (OBP23-28, OBP63-64) might originate from a single gene through a series of historic duplication events at least before divergence of Anopheles, Culex and Aedes. The microsynteny analyses indicate a very high synteny between An. sinensis and An. gambiae OBPs. OBP70 and OBP71 earlier classified under Plus-C in An. gambiae are recognized as belonging to the group Obp59a of the Classic subfamily, and OBP69 earlier classified under Plus-C has been moved to the Atypical subfamily in this study. The study established a basic information frame for further study of the OBP genes in insects as well as in An. sinensis. © 2016 Institute of Zoology, Chinese Academy of Sciences.

Annotation of Selaginella moellendorffii major intrinsic proteins and the evolution of the protein family in terrestrial plants

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Hanna Isa Anderberg

2012-02-01

Full Text Available Major intrinsic proteins (MIPs also called aquaporins form pores in membranes to facilitate the permeation of water and certain small polar solutes across membranes. MIPs are present in virtually every organism but are uniquely abundant in land plants. To elucidate the evolution and function of MIPs in terrestrial plants, the MIPs encoded in the genome of the spikemoss Selaginella moellendorffii were identified and analyzed. In total 19 MIPs were found in S. moellendorffii belonging to six of the seven MIP subfamilies previously identified in the moss Physcomitrella patens. Only three of the MIPs were classified as members of the conserved water specific plasma membrane intrinsic protein (PIP subfamily whereas almost half were found to belong to the diverse NOD26-like intrinsic protein (NIP subfamily permeating various solutes. The small number of PIPs in S. moellendorffii is striking compared to all other land plants and no other species has more NIPs than PIPs. Similar to moss, S. moellendorffii only has one type of tonoplast intrinsic protein (TIP. Based on ESTs from non-angiosperms we conclude that the specialized groups of TIPs present in higher plants are not found in primitive vascular plants but evolved later in a common ancestor of seed plants. We also note that the silicic acid permeable NIP2 group that has been reported from angiosperms appears at the same time. We suggest that the expansion of the number MIP isoforms in higher plants is primarily associated with an increase in the different types of specialized tissues rather than the emergence of vascular tissue per se and that the loss of subfamilies has been possible due to a functional overlap between some subfamilies.

Transcriptional analysis of the HeT-A retrotransposon in mutant and wild type stocks reveals high sequence variability at Drosophila telomeres and other unusual features

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Piñeyro David

2011-11-01

Full Text Available Abstract Background Telomere replication in Drosophila depends on the transposition of a domesticated retroelement, the HeT-A retrotransposon. The sequence of the HeT-A retrotransposon changes rapidly resulting in differentiated subfamilies. This pattern of sequence change contrasts with the essential function with which the HeT-A is entrusted and brings about questions concerning the extent of sequence variability, the telomere contribution of different subfamilies, and whether wild type and mutant Drosophila stocks show different HeT-A scenarios. Results A detailed study on the variability of HeT-A reveals that both the level of variability and the number of subfamilies are higher than previously reported. Comparisons between GIII, a strain with longer telomeres, and its parental strain Oregon-R indicate that both strains have the same set of HeT-A subfamilies. Finally, the presence of a highly conserved splicing pattern only in its antisense transcripts indicates a putative regulatory, functional or structural role for the HeT-A RNA. Interestingly, our results also suggest that most HeT-A copies are actively expressed regardless of which telomere and where in the telomere they are located. Conclusions Our study demonstrates how the HeT-A sequence changes much faster than previously reported resulting in at least nine different subfamilies most of which could actively contribute to telomere extension in Drosophila. Interestingly, the only significant difference observed between Oregon-R and GIII resides in the nature and proportion of the antisense transcripts, suggesting a possible mechanism that would in part explain the longer telomeres of the GIII stock.

Snf2 family gene distribution in higher plant genomes reveals DRD1 expansion and diversification in the tomato genome.

Science.gov (United States)

Bargsten, Joachim W; Folta, Adam; Mlynárová, Ludmila; Nap, Jan-Peter

2013-01-01

As part of large protein complexes, Snf2 family ATPases are responsible for energy supply during chromatin remodeling, but the precise mechanism of action of many of these proteins is largely unknown. They influence many processes in plants, such as the response to environmental stress. This analysis is the first comprehensive study of Snf2 family ATPases in plants. We here present a comparative analysis of 1159 candidate plant Snf2 genes in 33 complete and annotated plant genomes, including two green algae. The number of Snf2 ATPases shows considerable variation across plant genomes (17-63 genes). The DRD1, Rad5/16 and Snf2 subfamily members occur most often. Detailed analysis of the plant-specific DRD1 subfamily in related plant genomes shows the occurrence of a complex series of evolutionary events. Notably tomato carries unexpected gene expansions of DRD1 gene members. Most of these genes are expressed in tomato, although at low levels and with distinct tissue or organ specificity. In contrast, the Snf2 subfamily genes tend to be expressed constitutively in tomato. The results underpin and extend the Snf2 subfamily classification, which could help to determine the various functional roles of Snf2 ATPases and to target environmental stress tolerance and yield in future breeding.

Evolutionary history of the most speciose mammals: molecular phylogeny of muroid rodents.

OpenAIRE

Michaux, Johan; Reyes, A.; Catzeflis, F.

2001-01-01

Phylogenetic relationships between 32 species of rodents representing 14 subfamilies of Muridae and four subfamilies of Dipodidae were studied using sequences of the nuclear protein-coding genes Lecithin Cholesterol Acyl Transferase (LCAT) and von Willebrand Factor (vWF). An examination of some evolutionary properties of each data matrix indicates that the two genes are rather complementary, with lower rates of nonsynonymous substitutions for LCAT. Both markers exhibit a wide range of GC3 per...

Studies on taxonomy and distribution of Acridoidea (Orthoptera of Bihar, India

Directory of Open Access Journals (Sweden)

M.K. Usmani

2012-10-01

Full Text Available Thirty seven species of locusts and grasshoppers representing 26 genera, four tribes and 12 subfamilies belonging to the families Pyrgomorphidae, Catantopidae and Acrididae are reported from different localities of Bihar. Their distinguishing characters and bio-ecological data are provided along with keys to tribes and subfamilies. This paper comprising of distribution and field observation along with taxonomy of Acridoid fauna is the first of its kind from the state.

Perianth evolution in Ranunculaceae: are petals ancestral in the family?

OpenAIRE

Nadot S.; Sauquet H.; Damerval C.; Jabbour F.; Domenech B.

2016-01-01

Progress has been made recently towards the elucidation of phylogenetic relationships among subfamilies and tribes of the Ranunculaceae – the most recent hypothesis was published in 2016 by our team. Although relationships among the 10 tribes of the subfamily Ranunculoideae remain incompletely supported, this hypothesis provides an interesting framework to address the key issue of the ancestral vs. derived nature of a differentiated perianth within the family, and at the level of Ranunculales...

New species of Cerambycidae from Panama, with new distribution records (Coleoptera: Cerambycidae).

Science.gov (United States)

Bezark, Larry G; Tyson, William H; Schiff, Nathan M

2013-01-21

Two new species of Cerambycidae, Tessaropa elizabeth Bezark, sp. nov. (subfamily Cerambycinae, tribe Methiini ) and Anelaphus cordiforme Tyson, sp. nov. (subfamily Cerambycinae, tribe Elaphidiini), are described from the western part of the Darien, Panama. Nine new country records for Panama are reported for the following species: Adetus linsleyi Mar-tins & Galileo, Estola strandiella Breuning, Nubosoplatus inbio Swift, Paranisopodus heterotarsus Monné & Martins, Pempteurys sericans Bates, Rosalba costaricensis (Melzer), Tomopterus brevicornis Giesbert, Psapharochrus nigricans (Lameere), and Oedudes bifasciata (Bates).

Gene : CBRC-PABE-12-0253 [SEVENS

Lifescience Database Archive (English)

Full Text Available 1e-160 92% ref|NP_001002918.1| olfactory receptor, family 8, subfamily D, member 2 [Homo sapiens] sp|Q9GZM6|... receptor-like protein JCG2 [Homo sapiens] gb|AAG43386.1| olfactory receptor-like protein JCG2 [Homo sapi...ens] tpg|DAA04600.1| TPA_inf: olfactory receptor OR11-303 [Homo sapiens] gb|EAW67579....1| olfactory receptor, family 8, subfamily D, member 2 [Homo sapiens] 1e-159 92% MTTSNHSSGAEFNLAGLTQRPELQLP...VIAEGYLLTAMAYDCCVAICRPLLYNIVMFHRVCSIMLAVVYSLGFLGATVHTTRMSVLSFCRSHTVSHYFCDILPLLTLSCSSTHINEILLFIIGGVNTLAPIMAVL

Gene expression, cellular localisation and function of glutamine synthetase isozymes in wheat (Triticum aestivum L.)

DEFF Research Database (Denmark)

Bernard, Stéphanie M.; Møller, Anders Laurell Blom; Dionisio, Giuseppe

2008-01-01

). Phylogenetic analysis showed that the wheat GS sub-families together with the GS genes from other monocotyledonous species form four distinct clades. Immunolocalisation studies in leaves, stems and rachis in plants at flowering showed GS protein to be present in parenchyma, phloem companion and perifascicular......We present the first cloning and study of glutamine synthetase (GS) genes in wheat (Triticum aestivum L.). Based on sequence analysis, phylogenetic studies and mapping data, ten GS sequences were classified into four sub-families: GS2 (a, b and c), GS1 (a, b and c), GSr (1 and 2) and GSe (1 and 2...... sheath cells. In situ localisation confirmed that GS1 transcripts were present in the perifascicular sheath cells whilst those for GSr were confined to the vascular cells. Studies of the expression and protein profiles showed that all GS sub-families were differentially expressed in the leaves, peduncle...

Molecular dynamics investigations of regioselectivity of anionic/aromatic substrates by a family of enzymes: a case study of diclofenac binding in CYP2C isoforms.

Science.gov (United States)

Cui, Ying-Lu; Xu, Fang; Wu, Rongling

2016-06-29

The CYP2C subfamily is of particular importance in the metabolism of drugs, food toxins, and procarcinogens. Like other P450 subfamilies, 2C enzymes share a high sequence identity, but significantly contribute in different ways to hepatic capacity to metabolize drugs. They often metabolize the same substrate to more than one product with different catalytic sites. Because it is challenging to characterize experimentally, much still remains unknown about the reason for why the substrate regioselectivity of these closely related subfamily members is different. Here, we have investigated the structural features of CYP2C8, CYP2C9, and CYP2C19 bound with their shared substrate diclofenac to elucidate the underlying molecular mechanism for the substrate regioselectivity of CYP2C subfamily enzymes. The obtained results demonstrate how a sequence divergence for the active site residues causes heterogeneous variations in the secondary structures and in major tunnel selections, and further affects the shape and chemical properties of the substrate-binding site. Structural analysis and free energy calculations showed that the most important determinants of regioselectivity among the CYP2C isoforms are the geometrical features of the active sites, as well as the hydrogen bonds and the hydrophobic interactions, mainly presenting as the various locations of Arg108 and substitutions of Phe205 for Ile205 in CYP2C8. The MM-GB/SA calculations combined with PMF results accord well with the experimental KM values, bridging the gap between the theory and the experimentally observed results of binding affinity differences. The present study provides important insights into the structure-function relationships of CYP2C subfamily enzymes, the knowledge of ligand binding characteristics and key residue contributions could guide future experimental and computational work on the synthesis of drugs with better pharmacokinetic properties so that CYP interactions could be avoided.

Genome-wide analysis of the cellulose synthase-like (Csl) gene family in bread wheat (Triticum aestivum L.).

Science.gov (United States)

Kaur, Simerjeet; Dhugga, Kanwarpal S; Beech, Robin; Singh, Jaswinder

2017-11-03

Hemicelluloses are a diverse group of complex, non-cellulosic polysaccharides, which constitute approximately one-third of the plant cell wall and find use as dietary fibres, food additives and raw materials for biofuels. Genes involved in hemicellulose synthesis have not been extensively studied in small grain cereals. In efforts to isolate the sequences for the cellulose synthase-like (Csl) gene family from wheat, we identified 108 genes (hereafter referred to as TaCsl). Each gene was represented by two to three homeoalleles, which are named as TaCslXY_ZA, TaCslXY_ZB, or TaCslXY_ZD, where X denotes the Csl subfamily, Y the gene number and Z the wheat chromosome where it is located. A quarter of these genes were predicted to have 2 to 3 splice variants, resulting in a total of 137 putative translated products. Approximately 45% of TaCsl genes were located on chromosomes 2 and 3. Sequences from the subfamilies C and D were interspersed between the dicots and grasses but those from subfamily A clustered within each group of plants. Proximity of the dicot-specific subfamilies B and G, to the grass-specific subfamilies H and J, respectively, points to their common origin. In silico expression analysis in different tissues revealed that most of the genes were expressed ubiquitously and some were tissue-specific. More than half of the genes had introns in phase 0, one-third in phase 2, and a few in phase 1. Detailed characterization of the wheat Csl genes has enhanced the understanding of their structural, functional, and evolutionary features. This information will be helpful in designing experiments for genetic manipulation of hemicellulose synthesis with the goal of developing improved cultivars for biofuel production and increased tolerance against various stresses.

Structure of the Regulator of G Protein Signaling 8 (RGS8)-Gαq Complex: MOLECULAR BASIS FOR Gα SELECTIVITY.

Science.gov (United States)

Taylor, Veronica G; Bommarito, Paige A; Tesmer, John J G

2016-03-04

Regulator of G protein signaling (RGS) proteins interact with activated Gα subunits via their RGS domains and accelerate the hydrolysis of GTP. Although the R4 subfamily of RGS proteins generally accepts both Gαi/o and Gαq/11 subunits as substrates, the R7 and R12 subfamilies select against Gαq/11. In contrast, only one RGS protein, RGS2, is known to be selective for Gαq/11. The molecular basis for this selectivity is not clear. Previously, the crystal structure of RGS2 in complex with Gαq revealed a non-canonical interaction that could be due to interfacial differences imposed by RGS2, the Gα subunit, or both. To resolve this ambiguity, the 2.6 Å crystal structure of RGS8, an R4 subfamily member, was determined in complex with Gαq. RGS8 adopts the same pose on Gαq as it does when bound to Gαi3, indicating that the non-canonical interaction of RGS2 with Gαq is due to unique features of RGS2. Based on the RGS8-Gαq structure, residues in RGS8 that contact a unique α-helical domain loop of Gαq were converted to those typically found in R12 subfamily members, and the reverse substitutions were introduced into RGS10, an R12 subfamily member. Although these substitutions perturbed their ability to stimulate GTP hydrolysis, they did not reverse selectivity. Instead, selectivity for Gαq seems more likely determined by whether strong contacts can be maintained between α6 of the RGS domain and Switch III of Gαq, regions of high sequence and conformational diversity in both protein families. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

[Dental enamel prisms of Mesopithecus pentelicus Wagner, 1839, compared with recent cercopithecids (Primates: Cercopithecidae)].

Science.gov (United States)

Dostal, A; Zapfe, H

1986-01-01

The dental enamel prisms of Cercopithecidae were examined by scanning electron microscopy. The main task of this study was to show the prism morphology representatives of different genera as well as their comparison with the fossil Mesopithecus pentelicus Wagner, 1839. The method used to show the enamel prisms was to etch the tooth surface with hydrochloric acid. In this way the outlines of the prisms were better contrasted for the descriptive morphology of the prisms than in etching with phosphoric acid. Two types were determined, in accord with the systematic division into subfamilies. In the subfamily Cercopithecinae elongated slender prisms were dominating, some with pointed, others with truncated tops. Most characteristic of this type were Macaca and Cercopithecus. An exception was Papio hamadryas which had broader, rounded prisms. In this way it differed largely from P. anubis whose prisms were short and mostly triangular. A very interesting fact was that very different patterns were found in P. anubis and P. hamadryas, although these two species are regarded as only one species by many authors. The second subfamily, the Colobinae, was characterized by broader prisms with a rounded shape, nearly as long as wide. Exceptions of the 'Colobine type' were at first Colobus with prisms little longer than wide and secondly Nasalis, with mostly parallel sides and truncated tops of the prisms. The prism outlines of Mesopithecus showed the greatest similarity to those of Presbytis which represents the characteristic 'Colobine type'. This fact confirmed the actual systematic position of the fossil Mesopithecus within the subfamily Colobinae. In addition to previously known primitive features of Mesopithecus within the subfamily of Colobinae, we present here a further concrete, common feature with asiatic Colobines.

Molecular phylogeny of tribe Stachydeae (Lamiaceae subfamily Lamioideae)

DEFF Research Database (Denmark)

Salmaki, Yasaman; Zarre, Shahin; Ryding, Olof

2013-01-01

this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae...... subclades are congruent between the plastid and nuclear tree topologies, whereas their relative phylogenetic placements are often not. This level of plastid-nuclear incongruence suggests considerable impact of hybridization in the evolution of Stachydeae. (C) 2013 Elsevier Inc. All rights reserved....

The ERK MAP kinase-PEA3/ETV4-MMP-1 axis is operative in oesophageal adenocarcinoma

LENUS (Irish Health Repository)

Keld, Richard

2010-12-09

Abstract Background Many members of the ETS-domain transcription factor family are important drivers of tumourigenesis. In this context, their activation by Ras-ERK pathway signaling is particularly relevant to the tumourigenic properties of many ETS-domain transcription factors. The PEA3 subfamily of ETS-domain transcription factors have been implicated in tumour metastasis in several different cancers. Results Here, we have studied the expression of the PEA3 subfamily members PEA3\\/ETV4 and ER81\\/ETV1 in oesophageal adenocarcinomas and determined their role in oesophageal adenocarcinoma cell function. PEA3 plays an important role in controlling both the proliferation and invasive properties of OE33 oesophageal adenocarcinoma cells. A key target gene is MMP-1. The ERK MAP kinase pathway activates PEA3 subfamily members and also plays a role in these PEA3 controlled events, establishing the ERK-PEA3-MMP-1 axis as important in OE33 cells. PEA3 subfamily members are upregulated in human adenocarcinomas and expression correlates with MMP-1 expression and late stage metastatic disease. Enhanced ERK signaling is also more prevalent in late stage oesophageal adenocarcinomas. Conclusions This study shows that the ERK-PEA3-MMP-1 axis is upregulated in oesophageal adenocarcinoma cells and is a potentially important driver of the metastatic progression of oesophageal adenocarcinomas.

The major megadrile families of th e World reviewed again on their taxonomic types (Annelida: Oligochaeta: Megadrilacea

Directory of Open Access Journals (Sweden)

Blakemore, R. J.

2013-11-01

Full Text Available A critique of recent clado-molecular phylogenies notes shortcomings of starting materials, methods applied, and,therefore, their conclusions; hence this review. A new group, Exquisiclitellata, is newly defined as those ‘non-crassiclitellate’members of the superorder Megadrilacea (viz., Moniligastridae Claus, 1880, plus Alluroididae Michaelsen, 1900 andSyngenodrilidae Smith & Green, 1919. Support for restitution and elevation of American Diplocardiinae Michaelsen, 1900and Argilophilini Fender & McKey-Fender, 1990 are again raised. ICZN priority requires revival of Typhoeus Beddard, 1883over synonym Eutyphoeus Michaelsen, 1900 and the sub-family Typhoeinae (corr. of Typhaeinae Benham, 1890 is reestablished.Hoplochaetellinae sub-family nov. is proposed as a development of Octochaetidae s. lato in India.Wegeneriellinae sub-fam. nov. accommodates the holoic members of a restricted Neogastrini Csuzdi, 1996 from W. Africaand S. America. Caribbean family Exxidae Blakemore, 2000 and related Trigastrinae Michaelsen, 1900 are both retained. Acontingency table of Megascolecidae s. stricto sub-families and types is presented with some revived and a few new subfamiliesproposed, particularly from Australasia. These are Diporochaetinae, Megascolidesinae, Celeriellinae, andWoodwardiellinae sub-fams. nov. Synonymy of Perichaetidae Claus, 1880 over Megascolecidae Rosa, 1891 is deferred forreasons of nomenclatural stability. For the large African family Eudrilidae Claus, 1880, a new sub-family, Polytoreutinae, isadvanced and the status of abandoned Teleudrilini Michaelsen, 1891 and overlooked Hippoperidae Taylor, 1949 are noted.

Retrotransposons of the Tnt1B family are mobile in Nicotiana plumbaginifolia and can induce alternative splicing of the host gene upon insertion.

Science.gov (United States)

Leprinc, A S; Grandbastien, M A; Christian, M

2001-11-01

Active retrotransposons have been identified in Nicotiana plumbaginifolia by their ability to disrupt the nitrate reductase gene in chlorate-resistant mutants selected from protoplast-derived cultures. In mutants E23 and F97, two independent insertions of Tnp2, a new retrotransposon closely related to the tobacco Tnt1 elements, were detected in the nitrate reductase gene. These two Tnp2 elements are members of the Tnt1B subfamily which shows that Tnt1B elements can be active and mutagenic in the N. plumbaginifolia genome. Furthermore, these results suggest that Tnt1B is the most active family of Tntl elements in N. plumbaginifolia, whereas in tobacco only members of the Tnt1A subfamily were found inserted in the nitrate reductase gene. The transcriptional regulations of Tnp2 and Tnt1A elements are most probably different due to non-conserved U3 regions. Our results thus support the hypothesis that different Nicotiana species contain different active Tntl subfamilies and that only one active Tntl subfamily might be maintained in each of these species. The Tnp2 insertion found in the F97 mutant was found to be spliced out of the nitrate reductase mRNA by activation of cryptic donor and acceptor sites in the nitrate reductase and the Tnp2 sequences respectively.

Tracking Alu evolution in New World primates

Directory of Open Access Journals (Sweden)

Batzer Mark A

2005-10-01

Full Text Available Abstract Background Alu elements are Short INterspersed Elements (SINEs in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu sequences for loci specific to platyrrhine (New World primates. Results Branching patterns along an Alu sequence phylogeny indicate three major classes of platyrrhine-specific Alu sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; AluTa7, AluTa10, and AluTa15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of AluSc- and AluSp-type elements. This is a novel mode of origin for new Alu subfamilies. Conclusion The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.

Snf2 family gene distribution in higher plant genomes reveals DRD1 expansion and diversification in the tomato genome.

Directory of Open Access Journals (Sweden)

Joachim W Bargsten

Full Text Available As part of large protein complexes, Snf2 family ATPases are responsible for energy supply during chromatin remodeling, but the precise mechanism of action of many of these proteins is largely unknown. They influence many processes in plants, such as the response to environmental stress. This analysis is the first comprehensive study of Snf2 family ATPases in plants. We here present a comparative analysis of 1159 candidate plant Snf2 genes in 33 complete and annotated plant genomes, including two green algae. The number of Snf2 ATPases shows considerable variation across plant genomes (17-63 genes. The DRD1, Rad5/16 and Snf2 subfamily members occur most often. Detailed analysis of the plant-specific DRD1 subfamily in related plant genomes shows the occurrence of a complex series of evolutionary events. Notably tomato carries unexpected gene expansions of DRD1 gene members. Most of these genes are expressed in tomato, although at low levels and with distinct tissue or organ specificity. In contrast, the Snf2 subfamily genes tend to be expressed constitutively in tomato. The results underpin and extend the Snf2 subfamily classification, which could help to determine the various functional roles of Snf2 ATPases and to target environmental stress tolerance and yield in future breeding.

Crystal structure of the C3bot–RalA complex reveals a novel type of action of a bacterial exoenzyme

OpenAIRE

Pautsch, Alexander; Vogelsgesang, Martin; Tränkle, Jens; Herrmann, Christian; Aktories, Klaus

2005-01-01

C3 exoenzymes from bacterial pathogens ADP-ribosylate and inactivate low-molecular-mass GTPases of the Rho subfamily. Ral, a Ras subfamily GTPase, binds the C3 exoenzymes from Clostridium botulinum and C. limosum with high affinity without being a substrate for ADP ribosylation. In the complex, the ADP-ribosyltransferase activity of C3 is blocked, while binding of NAD and NAD-glycohydrolase activity remain. Here we report the crystal structure of C3 from C. botulinum in a complex with GDP-bou...

A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases

Institute of Scientific and Technical Information of China (English)

Qingshu Meng; Kaifu Chen; Lina Ma; Songnian Hu; Jun Yu

2011-01-01

Transposons are sequence elements widely distributed among genomes of all three kingdoms of life, providing genomic changes and playing significant roles in genome evolution. Trichomonas vaginalis is an excellent model system for transposon study since its genome ( ～ 160 Mb) has been sequenced and is composed of ～65% transposons and other repetitive elements. In this study, we primarily report the identification of Kolobok-type transposons (termed tvBac) in T. vaginalis and the results of transposase sequence analysis. We categorized 24 novel subfamilies of the Kolobok element, including one autonomous subfamily and 23 non-autonomous subfamilies. We also identified a novel H2CH motif in tvBac transposases based on multiple sequence alignment. In addition, we supposed that tvBac and Mutator transposons may have evolved independently from a common ancestor according to our phylogenetic analysis. Our results provide basic information for the understanding of the function and evolution of tvBac transposons in particular and other related transposon families in general.

Checklist of Recent thecideoid brachiopods from the Indian Ocean and Red Sea, with a description of a new species of Thecidellina from Europa Island and a re-description of T. blochmanni Dall from Christmas Island.

Science.gov (United States)

Logan, Alan; Hoffmann, Jana; Lüter, Carsten

2015-09-08

Compilation of a checklist of Recent thecideoid brachiopods from the Indian Ocean and Red Sea indicates that members of this superfamily are represented by a small number of species. The subfamily Lacazellinae is represented by Ospreyella maldiviana from the Maldive Islands but the presence of Lacazella cannot yet be confirmed in the Indian Ocean as the holotype of Lacazella mauritiana from Mauritius is lost. The subfamily Thecidellininae is represented by Thecidellina blochmanni from Christmas Island in the eastern Indian Ocean and the Red Sea while a new species T. europa is here described from Europa Island in the Mozambique Channel. The subfamily Minutellinae is represented by Minutella minuta from Samper Bank and Walters Bank in the south-western Indian Ocean and in the Red Sea. Since the holotype of Thecidellina blochmanni from Flying Fish Cove, Christmas Island is also lost, this species is re-described and illustrated mainly from topotypes in the Museum für Naturkunde, Berlin, from which a suggested neotype has been selected.

Revision of the subfamily Opiinae (Hymenoptera, Braconidae) from Hunan (China), including thirty-six new species and two new genera

Science.gov (United States)

Li, Xi-Ying; van Achterberg, Cornelis; Tan, Ji-Cai

2013-01-01

Abstract The species of the subfamily Opiinae (Hymenoptera: Braconidae) from Hunan (Oriental China) are revised and illustrated. Thirty-six new species are described: Apodesmia bruniclypealis Li & van Achterberg, sp. n., Apodesmia melliclypealis Li & van Achterberg, sp. n., Areotetes albiferus Li & van Achterberg, sp. n., Areotetes carinuliferus Li & van Achterberg, sp. n., Areotetes striatiferus Li & van Achterberg, sp. n., Coleopioides diversinotum Li & van Achterberg, sp. n., Coleopioides postpectalis Li & van Achterberg, sp. n., Fopius dorsopiferus Li, van Achterberg & Tan, sp. n., Indiopius chenae Li & van Achterberg, sp. n., Opiognathus aulaciferus Li & van Achterberg, sp. n., Opiognathus brevibasalis Li & van Achterberg, sp. n., Opius crenuliferus Li & van Achterberg, sp. n., Opius malarator Li, van Achterberg & Tan, sp. n., Opius monilipalpis Li & van Achterberg, sp. n., Opius pachymerus Li & van Achterberg, sp. n., Opius songi Li & van Achterberg, sp. n., Opius youi Li & van Achterberg, sp. n., Opius zengi Li & van Achterberg, sp. n., Phaedrotoma acuticlypeata Li & van Achterberg, sp. n., Phaedrotoma angiclypeata Li & van Achterberg, sp. n., Phaedrotoma antenervalis Li & van Achterberg, sp. n., Phaedrotoma depressiclypealis Li & van Achterberg, sp. n., Phaedrotoma flavisoma Li & van Achterberg, sp. n., Phaedrotoma nigrisoma Li & van Achterberg, sp. n., Phaedrotoma protuberator Li & van Achterberg, sp. n., Phaedrotoma rugulifera Li & van Achterberg, sp. n., Li & van Achterberg,Phaedrotoma striatinota Li & van Achterberg, sp. n., Phaedrotoma vermiculifera Li & van Achterberg, sp. n., Rhogadopsis latipennis Li & van Achterberg, sp. n., Rhogadopsis longicaudifera Li & van Achterberg, sp. n., Rhogadopsis maculosa Li, van Achterberg & Tan, sp. n., Rhogadopsis obliqua Li & van Achterberg, sp. n., Rhogadopsis sculpturator Li & van Achterberg, sp. n., Utetes longicarinatus Li & van Achterberg, sp. n. and Xynobius notauliferus Li & van Achterberg, sp. n. Areotetes

A putative autonomous 20.5 kb-CACTA transposon insertion in an F3'H allele identifies a new CACTA transposon subfamily in Glycine max

Directory of Open Access Journals (Sweden)

Vodkin Lila

2008-12-01

in the gray trichome allele t*. Conclusion The molecular characterization of a 20.5 kb insertion in the flavonoid 3'-hydroxylase (F3'H gene of a soybean gray pubescence allele (t* identified the structure of a CACTA transposon designated Tgmt*. Besides the terminal inverted repeats and subterminal repeated motifs,Tgmt* encoded a large gene with two putative functions that are required for excision and transposition of a CACTA element, a transposase and the DNA binding protein known to associate to the subterminal repeated motifs. The degree of dissimilarity between Tgmt* transposase and subterminal repeated motifs with those of previously characterized defective CACTA elements (Tgm1-7 were evidence of the existence of two subfamilies of CACTA transposons in soybean, an observation not previously reported in other plants. In addition, our analyses of a genetically active and potentially autonomous element sheds light on the complete structure of a soybean element that is useful for annotation of the repetitive fraction of the soybean genome sequence and may prove useful for transposon tagging or transposon display experiments in different genetic lines.

Chironomidae Fauna (Diptera-Insecta) of Gümüldür Stream (İzmir)

OpenAIRE

USTAOĞLU, Mustafa Ruşen; BALIK, Süleyman; TAŞDEMİR, Ayşe

2014-01-01

Samples were collected monthly from 10 different stations between April, 1993, and March, 1994, in order to determine the Chironomidae fauna of Gümüldür Stream in İzmir, Turkey. Ten species were found in the stream as determined from qualitative analyses of the samples. Of these, 5 species belong to the subfamily Orthocladiinae and the remaining 5 belong to the subfamily Chironominae. This is the first study reporting the existence of these species in Gümüldür Stream.

Canonical Transient Receptor Potential (TRPC) 1 Acts as a Negative Regulator for Vanilloid TRPV6-mediated Ca2+ Influx*

OpenAIRE

Schindl, Rainer; Fritsch, Reinhard; Jardin, Isaac; Frischauf, Irene; Kahr, Heike; Muik, Martin; Riedl, Maria Christine; Groschner, Klaus; Romanin, Christoph

2012-01-01

TRP proteins mostly assemble to homomeric channels but can also heteromerize, preferentially within their subfamilies. The TRPC1 protein is the most versatile member and forms various TRPC channel combinations but also unique channels with the distantly related TRPP2 and TRPV4. We show here a novel cross-family interaction between TRPC1 and TRPV6, a Ca2+ selective member of the vanilloid TRP subfamily. TRPV6 exhibited substantial co-localization and in vivo interaction with TRPC1 in HEK293 ce...

Inventory and general analysis of the ATP-binding cassette (ABC) gene superfamily in maize (Zea mays L.).

Science.gov (United States)

Pang, Kaiyuan; Li, Yanjiao; Liu, Menghan; Meng, Zhaodong; Yu, Yanli

2013-09-10

The metabolic functions of ATP-binding cassette (or ABC) proteins, one of the largest families of proteins presented in all organisms, have been investigated in many protozoan, animal and plant species. To facilitate more systematic and complicated studies on maize ABC proteins in the future, we present the first complete inventory of these proteins, including 130 open reading frames (ORFs), and provide general descriptions of their classifications, basic structures, typical functions, evolution track analysis and expression profiles. The 130 ORFs were assigned to eight subfamilies based on their structures and homological features. Five of these subfamilies consist of 109 proteins, containing transmembrane domains (TM) performing as transporters. The rest three subfamilies contain 21 soluble proteins involved in various functions other than molecular transport. A comparison of ABC proteins among nine selected species revealed either convergence or divergence in each of the ABC subfamilies. Generally, plant genomes contain far more ABC genes than animal genomes. The expression profiles and evolution track of each maize ABC gene were further investigated, the results of which could provide clues for analyzing their functions. Quantitative real-time polymerase chain reaction experiments (PCR) were conducted to detect induced expression in select ABC genes under several common stresses. This investigation provides valuable information for future research on stress tolerance in plants and potential strategies for enhancing maize production under stressful conditions. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair.

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Wu, Dong-Dong; Irwin, David M; Zhang, Ya-Ping

2008-08-23

Hair is unique to mammals. Keratin associated proteins (KRTAPs), which contain two major groups: high/ultrahigh cysteine and high glycine-tyrosine, are one of the major components of hair and play essential roles in the formation of rigid and resistant hair shafts. The KRTAP family was identified as being unique to mammals, and near-complete KRTAP gene repertoires for eight mammalian genomes were characterized in this study. An expanded KRTAP gene repertoire was found in rodents. Surprisingly, humans have a similar number of genes as other primates despite the relative hairlessness of humans. We identified several new subfamilies not previously reported in the high/ultrahigh cysteine KRTAP genes. Genes in many subfamilies of the high/ultrahigh cysteine KRTAP genes have evolved by concerted evolution with frequent gene conversion events, yielding a higher GC base content for these gene sequences. In contrast, the high glycine-tyrosine KRTAP genes have evolved more dynamically, with fewer gene conversion events and thus have a lower GC base content, possibly due to positive selection. Most of the subfamilies emerged early in the evolution of mammals, thus we propose that the mammalian ancestor should have a diverse KRTAP gene repertoire. We propose that hair content characteristics have evolved and diverged rapidly among mammals because of rapid divergent evolution of KRTAPs between species. In contrast, subfamilies of KRTAP genes have been homogenized within each species due to concerted evolution.

A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus).

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Churakov, Gennady; Smit, Arian F A; Brosius, Jürgen; Schmitz, Jürgen

2005-04-01

About half of the mammalian genome is composed of retroposons. Long interspersed elements (LINEs) and short interspersed elements (SINEs) are the most abundant repetitive elements and account for about 21% and 13% of the human genome, respectively. SINEs have been detected in all major mammalian lineages, except for the South American order Xenarthra, also termed Edentata (armadillos, anteaters, and sloths). Investigating this order, we discovered a novel high-copy-number family of tRNA derived SINEs in the nine-banded armadillo Dasypus novemcinctus, a species that successfully crossed the Central American land bridge to North America in the Pliocene. A specific computer algorithm was developed, and we detected and extracted 687 specific SINEs from databases. Termed DAS-SINEs, we further divided them into six distinct subfamilies. We extracted tRNA(Ala)-derived monomers, two types of dimers, and three subfamilies of chimeric fusion products of a tRNA(Ala) domain and an approximately 180-nt sequence of thus far unidentified origin. Comparisons of secondary structures of the DAS-SINEs' tRNA domains suggest selective pressure to maintain a tRNA-like D-arm structure in the respective founder RNAs, as shown by compensatory mutations. By analysis of subfamily-specific genetic variability, comparison of the proportion of direct repeats, and analysis of self-integrations as well as key events of dimerization and deletions or insertions, we were able to delineate the evolutionary history of the DAS-SINE subfamilies.

Cloning, characterization and tissue distribution of the rat ATP-binding cassette (ABC) transporter ABC2/ABCA2.

OpenAIRE

Zhao, L X; Zhou, C J; Tanaka, A; Nakata, M; Hirabayashi, T; Amachi, T; Shioda, S; Ueda, K; Inagaki, N

2000-01-01

The ABC1 (ABCA) subfamily of the ATP-binding cassette (ABC) transporter superfamily has a structural feature that distinguishes it from other ABC transporters. Here we report the cloning, molecular characterization and tissue distribution of ABC2/ABCA2, which belongs to the ABC1 subfamily. Rat ABC2 is a protein of 2434 amino acids that has 44.5%, 40.0% and 40.8% identity with mouse ABC1/ABCA1, human ABC3/ABCA3 and human ABCR/ABCA4 respectively. Immunoblot analysis showed that proteins of 260 ...

Monopsony in the labor market: Profit vs. Wage maximization

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Šuvaković Đorđe, Olgin

2007-01-01

Full Text Available This paper compares the efficiency of profit- and wage-maximizing (PM and WM monopsony in the labor market. We show that, both locally and globally, a PM monopsony may well be dominated by its WM twin, where the local and global dominance are defined with respect to a single (inverse labor supply function and a single family of such functions. This family is always divided in the two disjoint (subfamilies of the PM and WM dominance. We also analyze some major factors that explain the size of these (subfamilies. .

Molecular Mimicry Regulates ABA Signaling by SnRK2 Kinases and PP2C Phosphatases

OpenAIRE

Soon, Fen-Fen; Ng, Ley-Moy; Zhou, X. Edward; West, Graham M.; Kovach, Amanda; Tan, M. H. Eileen; Suino-Powell, Kelly M.; He, Yuanzheng; Xu, Yong; Chalmers, Michael J.; Brunzelle, Joseph S.; Zhang, Huiming; Yang, Huaiyu; Jiang, Hualiang; Li, Jun

2011-01-01

Abscisic acid (ABA) is an essential hormone for plants to survive environmental stresses. At the center of the ABA signaling network is a subfamily of type 2C protein phosphatases (PP2Cs), which form exclusive interactions with ABA receptors and subfamily 2 Snfl-related kinase (SnRK2s). Here, we report a SnRK2-PP2C complex structure, which reveals marked similarity in PP2C recognition by SnRK2 and ABA receptors. In the complex, the kinase activation loop docks into the active site of PP2C, wh...

Skull shapes of the Lissodelphininae: radiation, adaptation and asymmetry.

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Galatius, Anders; Goodall, R Natalie P

2016-06-01

Within Delphinidae, the sub-family Lissodelphininae consists of 8 Southern Ocean species and 2 North Pacific species. Lissodelphininae is a result of recent phylogenetic revisions based on molecular methods. Thus, morphological radiation within the taxon has not been investigated previously. The sub-family consists of ecologically diverse groups such as (1) the Cephalorhynchus genus of 4 small species inhabiting coastal and shelf waters, (2) the robust species in the Lagenorhynchus genus with the coastal La. australis, the offshore La. cruciger, the pelagic species La. obscurus and La. obliquidens, and (3) the morphologically aberrant genus Lissodelphis. Here, the shapes of 164 skulls from adults of all 10 species were compared using 3-dimensional geometric morphometrics. The Lissodelphininae skulls were supplemented by samples of Lagenorhynchus albirostris and Delphinus delphis to obtain a context for the variation found within the subfamily. Principal components analysis was used to map the most important components of shape variation on phylogeny. The first component of shape variation described an elongation of the rostrum, lateral and dorsoventral compression of the neurocranium and smaller temporal fossa. The two Lissodelphis species were on the high extreme of this spectrum, while Lagenorhynchus australis, La. cruciger and Cephalorhynchus heavisidii were at the low extreme. Along the second component, La. cruciger was isolated from the other species by its expanded neurocranium and concave facial profile. Shape variation supports the gross phylogenetic relationships proposed by recent molecular studies. However, despite the great diversity of ecology and external morphology within the subfamily, shape variation of the feeding apparatus was modest, indicating a similar mode of feeding across the subfamily. All 10 species were similar in their pattern of skull asymmetry, but interestingly, two species using narrowband high frequency clicks (La. cruciger and C

World Checklist of Opiliones species (Arachnida. Part 1: Laniatores – Travunioidea and Triaenonychoidea

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Adriano Kury

2014-11-01

Full Text Available Comprising more than 6500 species, Opiliones is the third most diverse order of Arachnida, after the megadiverse Acari and Araneae. The database referred here is part 1 of 12 of a project containing an intended worldwide checklist of species and subspecies of Opiliones as Darwin Core archives, and it includes the superfamilies Travunioidea and Triaenonychoidea. These two superfamilies are often treated together under the denomination of Insidiatores. In this Part 1, a total of 571 species and subspecies are listed. Briggsidae and Cladonychiidae are both downgraded to subfamilies of Travuniidae. Peltonychia Roewer, 1935 is an available name and senior synonym of Hadziana Roewer, 1935 and is herein revalidated. Seven genera of Triaenonychidae described by Lawrence between 1931 and 1933 originally failed to comply ICZN rules for availability (Art. 13.3. All of them only became available when Staręga (1992 designated a type species for each. Therefore, the correct authorships of Austromontia Lawrence, 1931, Biacumontia Lawrence, 1931, Graemontia Lawrence, 1931, Larifugella Lawrence, 1933, Mensamontia Lawrence, 1931, Monomontia Lawrence, 1931 and Rostromontia Lawrence, 1931 are all Staręga, 1992. Fumontana Shear, 1977, originally referred only to subfamily Triaenonychinae (as opposed to Soerensenellinae then and not corresponding to present Triaenonychinae, not to any tribe (which in turn correspond to modern subfamilies is herein included in the subfamily Triaenonychinae. Picunchenops Maury, 1988 originally not included in any tribe of Triaenonychidae, is herein included in the subfamily Triaenonychinae. Trojanella Karaman, 2005, originally ranked as Travunioidea incertae sedis, is herein included in the Travuniidae Travuniinae. Nuncia ovata Roewer, 1915 (synonymized with Triaenonyx cockayni Hogg, 1920 by Forster (1954, but with inverted precedence is here combined as Nuncia coriacea ovata Roewer, 1915 as correct senior synonym instead of

Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family.

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He, Shunping; Mayden, Richard L; Wang, Xuzheng; Wang, Wei; Tang, Kevin L; Chen, Wei-Jen; Chen, Yiyu

2008-03-01

The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis

Distributional patterns and possible origin of leafhoppers (Homoptera, Cicadellidae

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Mervin W. Nielson

2000-03-01

Full Text Available The zoogeographical distribution of 42 cicadellid subfamilies and their assigned tribes and genera is compiled with distributional maps and proposed dispersal pathways of genera that are shared interzoogeographically. Possible origin of the subfamilies and tribes is proposed in an ancestral context from which the more modern extant groups evolved whereas origin of genera is in a more modern context. Notwithstanding their complex biogeography, the distributional data of the higher groups indicate that all of the cosmopolitan and near cosmopolitan subfamilies arose during early Cretaceous or possibly the late Jurassic period (140-116 m.y.a. when continental drift was in its early stages. Nearly all of the New World and some Old World subfamilies are considered of more recent origin (late Cretaceous-Tertiary. Ninety percent of the known genera (2,126 are endemic to their respective zoogeographical region and subregion, thus indicating relatively high host specificity and low rate of dispersal. The majority (76% of known extant genera are pantropical in origin, suggesting early or possible Gondwanaland origin of their ancestors. Dispersal pathways of genera shared by more than one zoogeographical region were generally south to north (Neotropical/Nearctic, Oriental/Palaearctic or west to east (Palaearctic/Nearctic, Oriental/Australian, from regions of high diversity to regions of low diversity and from warmer climates to cooler climates. The most diverse and richest leafhopper fauna are present in the Neotropical and Ethiopian regions although taxal affinities between them are poorest. The most depauperate fauna are in the Nearctic region and in Australia, reflecting the impact of isolating and ecological factors on distribution and radiation. Ecological barriers were more evident between the Ethiopian and Oriental fauna than between any other zoogeographical combination. Taxal affinities appeared to be correlated with close continental proximities

Evolutionary history of the most speciose mammals: molecular phylogeny of muroid rodents.

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Michaux, J; Reyes, A; Catzeflis, F

2001-11-01

Phylogenetic relationships between 32 species of rodents representing 14 subfamilies of Muridae and four subfamilies of Dipodidae were studied using sequences of the nuclear protein-coding genes Lecithin Cholesterol Acyl Transferase (LCAT) and von Willebrand Factor (vWF). An examination of some evolutionary properties of each data matrix indicates that the two genes are rather complementary, with lower rates of nonsynonymous substitutions for LCAT. Both markers exhibit a wide range of GC3 percentages (55%-89%), with several taxa above 70% GC3 for vWF, which indicates that those exonic regions might belong to the richest class of isochores. The primary sequence data apparently harbor few saturations, except for transitions on third codon positions for vWF, as indicated by comparisons of observed and expected pairwise values of substitutions. Phylogenetic trees based on 1,962 nucleotidic sites from the two genes indicate that the 14 Muridae subfamilies are organized into five major lineages. An early isolation leads to the clade uniting the fossorial Spalacinae and semifossorial Rhizomyinae with a strong robustness. The second lineage includes a series of African taxa representing nesomyines, dendromurines, cricetomyines, and the sole living member of mystromyines. The third one comprises only the mouselike hamster CALOMYSCUS: The fourth clade represents the cricetines, myospalacines, sigmodontines, and arvicolines, whereas the fifth one comprises four "traditional" subfamilies (Gerbillinae, Murinae, Otomyinae, and Acomyinae). Within these groups, we confirm the monophyly of almost all studied subfamilies, namely, Spalacinae, Rhizomyinae, Nesomyinae, Cricetomyinae, Arvicolinae, Sigmodontinae, Cricetinae, Gerbillinae, Acomyinae, and Murinae. Finally, we present evidence that the sister group of Acomyinae is Gerbillinae, and we confirm a nested position of Myospalacinae within Cricetinae and Otomyinae within Murinae. From a biogeographical point of view, the five main

The relationships within the Chaitophorinae and Drepanosiphinae (Hemiptera, Aphididae) inferred from molecular-based phylogeny and comprehensive morphological data

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Wieczorek, Karina; Lachowska-Cierlik, Dorota; Kajtoch, Łukasz; Kanturski, Mariusz

2017-01-01

The Chaitophorinae is a bionomically diverse Holarctic subfamily of Aphididae. The current classification includes two tribes: the Chaitophorini associated with deciduous trees and shrubs, and Siphini that feed on monocotyledonous plants. We present the first phylogenetic hypothesis for the subfamily, based on molecular and morphological datasets. Molecular analyses were based on the mitochondrial gene cytochrome oxidase subunit I (COI) and the nuclear gene elongation factor-1α (EF-1α). Phylogenetic inferences were obtained individually on each of genes and joined alignments using Bayesian inference (BI) and Maximum likelihood (ML). In phylogenetic trees reconstructed on the basis of nuclear and mitochondrial genes as well as a morphological dataset, the monophyly of Siphini and the genus Chaitophorus was supported. Periphyllus forms independent lineages from Chaitophorus and Siphini. Within this genus two clades comprising European and Asiatic species, respectively, were indicated. Concerning relationships within the subfamily, EF-1α and joined COI and EF-1α genes analysis strongly supports the hypothesis that Chaitophorini do not form a monophyletic clade. Periphyllus is a sister group to a clade containing Chaitophorus and Siphini. The Asiatic unit of Periphyllus also includes Trichaitophorus koyaensis. The analysis of morphological dataset under equally weighted parsimony also supports the view that Chaitophorini is an artificial taxon, as Lambersaphis pruinosae and Pseudopterocomma hughi, both traditionally included in the Chaitophorini, formed independent lineages. COI analyses support consistent groups within the subfamily, but relationships between groups are poorly resolved. These analyses were extended to include the species of closely related and phylogenetically unstudied subfamily Drepanosiphinae, which produced congruent results. Genera Drepanosiphum and Depanaphis are monophyletic and sister. The position of Yamatocallis tokyoensis differs in the

Evolution of light-harvesting complex proteins from Chl c-containing algae

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Puerta M Virginia

2011-04-01

Full Text Available Abstract Background Light harvesting complex (LHC proteins function in photosynthesis by binding chlorophyll (Chl and carotenoid molecules that absorb light and transfer the energy to the reaction center Chl of the photosystem. Most research has focused on LHCs of plants and chlorophytes that bind Chl a and b and extensive work on these proteins has uncovered a diversity of biochemical functions, expression patterns and amino acid sequences. We focus here on a less-studied family of LHCs that typically bind Chl a and c, and that are widely distributed in Chl c-containing and other algae. Previous phylogenetic analyses of these proteins suggested that individual algal lineages possess proteins from one or two subfamilies, and that most subfamilies are characteristic of a particular algal lineage, but genome-scale datasets had revealed that some species have multiple different forms of the gene. Such observations also suggested that there might have been an important influence of endosymbiosis in the evolution of LHCs. Results We reconstruct a phylogeny of LHCs from Chl c-containing algae and related lineages using data from recent sequencing projects to give ~10-fold larger taxon sampling than previous studies. The phylogeny indicates that individual taxa possess proteins from multiple LHC subfamilies and that several LHC subfamilies are found in distantly related algal lineages. This phylogenetic pattern implies functional differentiation of the gene families, a hypothesis that is consistent with data on gene expression, carotenoid binding and physical associations with other LHCs. In all probability LHCs have undergone a complex history of evolution of function, gene transfer, and lineage-specific diversification. Conclusion The analysis provides a strikingly different picture of LHC diversity than previous analyses of LHC evolution. Individual algal lineages possess proteins from multiple LHC subfamilies. Evolutionary relationships showed

Guía para la identificación genérica de larvas de quironómidos (Diptera: Chironomidae de la Sabana de Bogotá. III subfamilias Tanypodinae, Podonominae y Diamesinae

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Ruiz Moreno Jeanet Liliana

2000-07-01

Full Text Available A diagnosis of larvae in the subfamilies Tanypodinae and Podonominae (Chironomidae is provided, based on macroscopic and microscopic characters. A key to the genera recorded in streams of the Sabana de Bogotá and surrounding mountains is presented. Additionally, diagnoses are given for the genera Podonomus and Parochlus of the subfamily Podonominae and the genus araheptagyia, of the subfamily Diamesinae.Se presentan diagnosis de las subfamilias Tanypodinae y Podonominae (Diptera: Chironomidael, incluyendo características macroscópicas que diferencian las larvas de la subfamilia y microscópicas que permiten diferenciar los géneros, que hasta el momento se han encontrado en las aguas corrientes de la sabana de Bogotá y sus montañas circundantes. Además, se presenta una clave para la identificación de los diez géneros registrados para la subfamilia Tanypodinae, así como una diagnosis de los géneros: Podonomus y Parochlus, de la subfamilia Podominae y el género Paraheptagyia, de la subfamilia Diamesinae.

Molecular Evolution and Expansion Analysis of the NAC Transcription Factor in Zea mays

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Fan, Kai; Wang, Ming; Miao, Ying; Ni, Mi; Bibi, Noreen; Yuan, Shuna; Li, Feng; Wang, Xuede

2014-01-01

NAC (NAM, ATAF1, 2 and CUC2) family is a plant-specific transcription factor and it controls various plant developmental processes. In the current study, 124 NAC members were identified in Zea mays and were phylogenetically clustered into 13 distinct subfamilies. The whole genome duplication (WGD), especially an additional WGD event, may lead to expanding ZmNAC members. Different subfamily has different expansion rate, and NAC subfamily preference was found during the expansion in maize. Moreover, the duplication events might occur after the divergence of the lineages of Z. mays and S. italica, and segmental duplication seemed to be the dominant pattern for the gene duplication in maize. Furthermore, the expansion of ZmNAC members may be also related to gain and loss of introns. Besides, the restriction of functional divergence was discovered after most of the gene duplication events. These results could provide novel insights into molecular evolution and expansion analysis of NAC family in maize, and advance the NAC researches in other plants, especially polyploid plants. PMID:25369196

Pollen-expressed F-box gene family and mechanism of S-RNase-based gametophytic self-incompatibility (GSI) in Rosaceae.

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Sassa, Hidenori; Kakui, Hiroyuki; Minamikawa, Mai

2010-03-01

Many species of Rosaceae, Solanaceae, and Plantaginaceae exhibit S-RNase-based self-incompatibility (SI) in which pistil-part specificity is controlled by S locus-encoded ribonuclease (S-RNase). Although recent findings revealed that S locus-encoded F-box protein, SLF/SFB, determines pollen-part specificity, how these pistil- and pollen-part S locus products interact in vivo and elicit the SI reaction is largely unclear. Furthermore, genetic studies suggested that pollen S function can differ among species. In Solanaceae and the rosaceous subfamily Maloideae (e.g., apple and pear), the coexistence of two different pollen S alleles in a pollen breaks down SI of the pollen, a phenomenon known as competitive interaction. However, competitive interaction seems not to occur in the subfamily Prunoideae (e.g., cherry and almond) of Rosaceae. Furthermore, the effect of the deletion of pollen S seems to vary among taxa. This review focuses on the potential differences in pollen-part function between subfamilies of Rosaceae, Maloideae, and Prunoideae, and discusses implications for the mechanistic divergence of the S-RNase-based SI.

Genome-wide identification, functional and evolutionary analysis of terpene synthases in pineapple.

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Chen, Xiaoe; Yang, Wei; Zhang, Liqin; Wu, Xianmiao; Cheng, Tian; Li, Guanglin

2017-10-01

Terpene synthases (TPSs) are vital for the biosynthesis of active terpenoids, which have important physiological, ecological and medicinal value. Although terpenoids have been reported in pineapple (Ananas comosus), genome-wide investigations of the TPS genes responsible for pineapple terpenoid synthesis are still lacking. By integrating pineapple genome and proteome data, twenty-one putative terpene synthase genes were found in pineapple and divided into five subfamilies. Tandem duplication is the cause of TPS gene family duplication. Furthermore, functional differentiation between each TPS subfamily may have occurred for several reasons. Sixty-two key amino acid sites were identified as being type-II functionally divergence between TPS-a and TPS-c subfamily. Finally, coevolution analysis indicated that multiple amino acid residues are involved in coevolutionary processes. In addition, the enzyme activity of two TPSs were tested. This genome-wide identification, functional and evolutionary analysis of pineapple TPS genes provide a new insight into understanding the roles of TPS family and lay the basis for further characterizing the function and evolution of TPS gene family. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diversity of Braconidae (Insecta, Hymenoptera of the Parque Natural Municipal de Porto Velho, Rondonia, Brazil

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Sian de Souza Gadelha

2012-12-01

Full Text Available Braconidae is a highly diversified family of Hymenoptera and usually known by their role in biological control both in agricultural and natural ecosystems. Despite of that, little is known about its diversity in the Amazon region. The present work inventoried the braconid fauna of an Open Ombrophylous Forest with Palm Trees of the Parque Natural Municipal de Porto Velho, RO. Insects were collect from June/2008 to May/2009 using six Malaise traps in different parts of the reserve. A total of 377 wasps were captured, 17 subfamilies and 56 genera identified. Braconinae, Microgastrinae, Doryctinae and Rogadinae subfamilies were very abundant, and also the genera Aleiodes, Bracon, Capitonius, Compsobracon, Heterospilus, Hymenochaonia, Opius, Pedinotus, Rogas and Stantonia. The calculated Shannon diversity index was 2.15 and 3.3 for subfamily and genera, respectively, which were, generally, higher than the values found for other regions in Brazil. Generally, parasitoids were more abundant during the rainy season. The present work contributes with new genera records and faunistic data of Braconidae in Rondonia State, western Amazon.

The microRNA-200 family coordinately regulates cell adhesion and proliferation in hair morphogenesis.

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Hoefert, Jaimee E; Bjerke, Glen A; Wang, Dongmei; Yi, Rui

2018-06-04

The microRNA (miRNA)-200 (miR-200) family is highly expressed in epithelial cells and frequently lost in metastatic cancer. Despite intensive studies into their roles in cancer, their targets and functions in normal epithelial tissues remain unclear. Importantly, it remains unclear how the two subfamilies of the five-miRNA family, distinguished by a single nucleotide within the seed region, regulate their targets. By directly ligating miRNAs to their targeted mRNA regions, we identify numerous miR-200 targets involved in the regulation of focal adhesion, actin cytoskeleton, cell cycle, and Hippo/Yap signaling. The two subfamilies bind to largely distinct target sites, but many genes are coordinately regulated by both subfamilies. Using inducible and knockout mouse models, we show that the miR-200 family regulates cell adhesion and orientation in the hair germ, contributing to precise cell fate specification and hair morphogenesis. Our findings demonstrate that combinatorial targeting of many genes is critical for miRNA function and provide new insights into miR-200's functions. © 2018 Hoefert et al.

Genome-wide identification of Jatropha curcas aquaporin genes and the comparative analysis provides insights into the gene family expansion and evolution in Hevea brasiliensis

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Zhi eZou

2016-03-01

Full Text Available Aquaporins (AQPs are channel-forming integral membrane proteins that transport water and other small solutes across biological membranes. Despite the vital role of AQPs, to date, little is known in physic nut (Jatropha curcas L., Euphorbiaceae, an important non-edible oilseed crop with great potential for the production of biodiesel. In this study, 32 AQP genes were identified from the physic nut genome and the family number is relatively small in comparison to 51 in another Euphorbiaceae plant, rubber tree (Hevea brasiliensis Muell. Arg.. Based on the phylogenetic analysis, the JcAQPs were assigned to five subfamilies, i.e., 9 plasma membrane intrinsic proteins (PIPs, 9 tonoplast intrinsic proteins (TIPs, 8 NOD26-like intrinsic proteins (NIPs, 2 X intrinsic proteins (XIPs and 4 small basic intrinsic proteins (SIPs. Like rubber tree and other plant species, functional prediction based on the aromatic/arginine selectivity filter, Froger’s positions and specificity-determining positions showed a remarkable difference in substrate specificity among subfamilies of JcAQPs. Genome-wide comparative analysis revealed the specific expansion of PIP and TIP subfamilies in rubber tree and the specific gene loss of the XIP subfamily in physic nut. Furthermore, by analyzing deep transcriptome sequencing data, the expression evolution especially the expression divergence of duplicated HbAQP genes was also investigated and discussed. Results obtained from this study not only provide valuable information for future functional analysis and utilization of Jc/HbAQP genes, but also provide a useful reference to survey the gene family expansion and evolution in Euphorbiaceae plants and other plant species.

Arabidopsis thaliana AMY3 Is a Unique Redox-regulated Chloroplastic α-Amylase

DEFF Research Database (Denmark)

Seung, David; Thalmann, Matthias; Sparla, Francesca

2013-01-01

α-Amylases are glucan hydrolases that cleave α-1,4-glucosidic bonds in starch. In vascular plants, α-amylases can be classified into three subfamilies. Arabidopsis has one member of each subfamily. Among them, only AtAMY3 is localized in the chloroplast. We expressed and purified AtAMY3 from...... to be dependent on a conserved aspartic acid residue (Asp666), identified as the catalytic nucleophile in other plant α-amylases such as the barley AMY1. AtAMY3 released small linear and branched glucans from Arabidopsis starch granules, and the proportion of branched glucans increased after the predigestion...

A chromosomal analysis of four species of Chilean Chrysomelinae (Coleoptera, Chrysomelidae).

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Petitpierre, Eduard; Elgueta, Mario

2012-01-01

Four species of Chilean leaf beetles in the subfamily Chrysomelinae have been cytogenetically analyzed, Blaptea elguetai Petitpierre, 2011, Henicotherus porteri Bréthes, 1929 and Jolivetia obscura (Philippi, 1864) show 2n = 28 chromosomes and a 13 + Xyp male meioformula, and Pataya nitida (Philippi, 1864) has the highest number of 2n = 38 chromosomes. The karyotype of Henicotherus porteri is made of mostly small meta/submetacentric chromosomes, and that of Jolivetia obscura displays striking procentric blocks of heterochromatin at pachytene autosomic bivalents using conventional staining. These findings are discussed in relation to previous cytogenetic data and current taxonomy of the subfamily.

A remarkable new genus of Protosmylinae (Neuroptera: Osmylidae) from late Eocene Florissant, Colorado.

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Makarkin, Vladimir N

2017-05-18

Pseudosmylidia relicta gen. et sp. nov. (Neuroptera: Osmylidae) is described from the late Eocene of Florissant (U.S.A., Colorado). It is assigned to the subfamily Protosmylinae based on the presence of two venational features characteristic of the subfamily: most crossveins in the radial to intramedial spaces of the forewing are arranged in four gradate series, and CuP is short and simple or forked only once in the hind wing. This genus is remarkable by CuP in the forewing bearing few pectinate branches. This is the only genus of extant and Cenozoic fossil Osmylidae in which this plesiomorphic condition is retained.

Children under 5 in Families and Subfamilies in 1990

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U.S. Environmental Protection Agency — Variable was created as part of a set of indicators that demonstrate links between the condition of natural areas and human concerns and that quantify dependencies...

The actin multigene family of Paramecium tetraurelia

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Wagner Erika

2007-03-01

Full Text Available Abstract Background A Paramecium tetraurelia pilot genome project, the subsequent sequencing of a Megabase chromosome as well as the Paramecium genome project aimed at gaining insight into the genome of Paramecium. These cells display a most elaborate membrane trafficking system, with distinct, predictable pathways in which actin could participate. Previously we had localized actin in Paramecium; however, none of the efforts so far could proof the occurrence of actin in the cleavage furrow of a dividing cell, despite the fact that actin is unequivocally involved in cell division. This gave a first hint that Paramecium may possess actin isoforms with unusual characteristics. The genome project gave us the chance to search the whole Paramecium genome, and, thus, to identify and characterize probably all actin isoforms in Paramecium. Results The ciliated protozoan, P. tetraurelia, contains an actin multigene family with at least 30 members encoding actin, actin-related and actin-like proteins. They group into twelve subfamilies; a large subfamily with 10 genes, seven pairs and one trio with > 82% amino acid identity, as well as three single genes. The different subfamilies are very distinct from each other. In comparison to actins in other organisms, P. tetraurelia actins are highly divergent, with identities topping 80% and falling to 30%. We analyzed their structure on nucleotide level regarding the number and position of introns. On amino acid level, we scanned the sequences for the presence of actin consensus regions, for amino acids of the intermonomer interface in filaments, for residues contributing to ATP binding, and for known binding sites for myosin and actin-specific drugs. Several of those characteristics are lacking in several subfamilies. The divergence of P. tetraurelia actins and actin-related proteins between different P. tetraurelia subfamilies as well as with sequences of other organisms is well represented in a phylogenetic

Insertion and deletion polymorphisms of the ancient AluS family in the human genome.

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Kryatova, Maria S; Steranka, Jared P; Burns, Kathleen H; Payer, Lindsay M

2017-01-01

Polymorphic Alu elements account for 17% of structural variants in the human genome. The majority of these belong to the youngest AluY subfamilies, and most structural variant discovery efforts have focused on identifying Alu polymorphisms from these currently retrotranspositionally active subfamilies. In this report we analyze polymorphisms from the evolutionarily older AluS subfamily, whose peak activity was tens of millions of years ago. We annotate the AluS polymorphisms, assess their likely mechanism of origin, and evaluate their contribution to structural variation in the human genome. Of 52 previously reported polymorphic AluS elements ascertained for this study, 48 were confirmed to belong to the AluS subfamily using high stringency subfamily classification criteria. Of these, the majority (77%, 37/48) appear to be deletion polymorphisms. Two polymorphic AluS elements (4%) have features of non-classical Alu insertions and one polymorphic AluS element (2%) likely inserted by a mechanism involving internal priming. Seven AluS polymorphisms (15%) appear to have arisen by the classical target-primed reverse transcription (TPRT) retrotransposition mechanism. These seven TPRT products are 3' intact with 3' poly-A tails, and are flanked by target site duplications; L1 ORF2p endonuclease cleavage sites were also observed, providing additional evidence that these are L1 ORF2p endonuclease-mediated TPRT insertions. Further sequence analysis showed strong conservation of both the RNA polymerase III promoter and SRP9/14 binding sites, important for mediating transcription and interaction with retrotransposition machinery, respectively. This conservation of functional features implies that some of these are fairly recent insertions since they have not diverged significantly from their respective retrotranspositionally competent source elements. Of the polymorphic AluS elements evaluated in this report, 15% (7/48) have features consistent with TPRT-mediated insertion

FIRST RECORD OF FOSSIL CYSTOPHORINAE (CARNIVORA, PHOCIDAE: MIDDLE MIOCENE SEALS FROM THE NORTHERN PARATETHYS

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IRINA A. KORETSKY

2013-11-01

Full Text Available Despite a long history of phocid studies, no fossil members of the Subfamily Cystophorinae have ever been described. New fossil material from the Middle Sarmatian (11.2-12.3 Ma in the Paratethyan Basin of Ukraine allows emended diagnoses and redescriptions to help clarify phylogenetic relationships within the Family Phocidae. After cladistic and morphological analyses of the material, a new genus ( Pachyphoca  was erected, with two new species of extinct fossil true seals ( Pachyphoca ukrainica and Pachyphoca chapskii , belonging to the Subfamily Cystophorinae. This new material shows exceptional pachyosteosclerotic bones, which is uncommon for the family as a whole. The new Miocene genus shares numerous characters with several Recent species of Cystophora and Mirounga , providing the first opportunity to study sexual dimorphism of limb bones and mandibles in the Subfamily Cystophorinae. Sexual dimorphism in postcranial bones and mandibles in living members of Cystophorinae is more obvious than in other representatives of true seals. Examination of anatomical traits demonstrated that both new species are more primitive and better adapted for terrestrial locomotion than any living representatives of Cystophorinae. The smaller Pachyphoca ukrainica is more adapted to terrestrial locomotion than its larger relative, P . chapskii . Phylogenetic analysis suggests that seals with 10 incisors (Phocinae are more primitive than those with 8 (Monachinae, and that Monachinae are more primitive than seals with 6 incisors (Cystophorinae.These findings indicate that the Subfamily Cystophorinae includes not only elephant and hooded seals, but also the two new Middle Sarmatian pachyosteosclerotic seals. 

Genome-Wide Analysis of Oleosin Gene Family in 22 Tree Species: An Accelerator for Metabolic Engineering of BioFuel Crops and Agrigenomics Industrial Applications?

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Cao, Heping

2015-09-01

Trees contribute to enormous plant oil reserves because many trees contain 50%-80% of oil (triacylglycerols, TAGs) in the fruits and kernels. TAGs accumulate in subcellular structures called oil bodies/droplets, in which TAGs are covered by low-molecular-mass hydrophobic proteins called oleosins (OLEs). The OLEs/TAGs ratio determines the size and shape of intracellular oil bodies. There is a lack of comprehensive sequence analysis and structural information of OLEs among diverse trees. The objectives of this study were to identify OLEs from 22 tree species (e.g., tung tree, tea-oil tree, castor bean), perform genome-wide analysis of OLEs, classify OLEs, identify conserved sequence motifs and amino acid residues, and predict secondary and three-dimensional structures in tree OLEs and OLE subfamilies. Data mining identified 65 OLEs with perfect conservation of the "proline knot" motif (PX5SPX3P) from 19 trees. These OLEs contained >40% hydrophobic amino acid residues. They displayed similar properties and amino acid composition. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that these proteins could be classified into five OLE subfamilies. There were distinct patterns of sequence conservation among the OLE subfamilies and within individual tree species. Computational modeling indicated that OLEs were composed of at least three α-helixes connected with short coils without any β-strand and that they exhibited distinct 3D structures and ligand binding sites. These analyses provide fundamental information in the similarity and specificity of diverse OLE isoforms within the same subfamily and among the different species, which should facilitate studying the structure-function relationship and identify critical amino acid residues in OLEs for metabolic engineering of tree TAGs.

Molecular phylogeny of microhylid frogs (Anura: Microhylidae) with emphasis on relationships among New World genera

Science.gov (United States)

2012-01-01

Background Over the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e., incertae sedis). Results One mitochondrial and three nuclear genes (about 2.8 kb) were sequenced to assess phylogenetic relationships. We utilized an unprecedented sampling of 200 microhylid taxa representing 91% of currently recognized subfamilies and 95% of New World genera. Our analyses do not fully resolve relationships among subfamilies supporting previous studies that have suggested a rapid early diversification of this clade. We observed a close relationship between Synapturanus and Otophryne of the subfamily Otophryninae. Within the subfamily Gastrophryninae relationships between genera were well resolved. Conclusion Otophryninae is distantly related to all other New World microhylids that were recovered as a monophyletic group, Gastrophryninae. Within Gastrophryninae, five genera were recovered as non-monophyletic; we propose taxonomic re-arrangements to render all genera monophyletic. This hypothesis of relationships and updated classification for New World microhylids may serve as a guide to better understand the evolutionary history of this group that is apparently subject to convergent morphological evolution and chromosome reduction. Based on a divergence analysis calibrated with hypotheses from previous studies and fossil data, it appears that microhylid genera inhabiting the New World originated during a period of gradual cooling from the late Oligocene to mid Miocene. PMID:23228209

Molecular phylogeny of microhylid frogs (Anura: Microhylidae) with emphasis on relationships among New World genera.

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de Sá, Rafael O; Streicher, Jeffrey W; Sekonyela, Relebohile; Forlani, Mauricio C; Loader, Simon P; Greenbaum, Eli; Richards, Stephen; Haddad, Célio F B

2012-12-10

Over the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e., incertae sedis). One mitochondrial and three nuclear genes (about 2.8 kb) were sequenced to assess phylogenetic relationships. We utilized an unprecedented sampling of 200 microhylid taxa representing 91% of currently recognized subfamilies and 95% of New World genera. Our analyses do not fully resolve relationships among subfamilies supporting previous studies that have suggested a rapid early diversification of this clade. We observed a close relationship between Synapturanus and Otophryne of the subfamily Otophryninae. Within the subfamily Gastrophryninae relationships between genera were well resolved. Otophryninae is distantly related to all other New World microhylids that were recovered as a monophyletic group, Gastrophryninae. Within Gastrophryninae, five genera were recovered as non-monophyletic; we propose taxonomic re-arrangements to render all genera monophyletic. This hypothesis of relationships and updated classification for New World microhylids may serve as a guide to better understand the evolutionary history of this group that is apparently subject to convergent morphological evolution and chromosome reduction. Based on a divergence analysis calibrated with hypotheses from previous studies and fossil data, it appears that microhylid genera inhabiting the New World originated during a period of gradual cooling from the late Oligocene to mid Miocene.

A new highly conserved antibiotic sensing/resistance pathway in firmicutes involves an ABC transporter interplaying with a signal transduction system.

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Stéphanie Coumes-Florens

2011-01-01

Full Text Available Signal transduction systems and ABC transporters often contribute jointly to adaptive bacterial responses to environmental changes. In Bacillus subtilis, three such pairs are involved in responses to antibiotics: BceRSAB, YvcPQRS and YxdJKLM. They are characterized by a histidine kinase belonging to the intramembrane sensing kinase family and by a translocator possessing an unusually large extracytoplasmic loop. It was established here using a phylogenomic approach that systems of this kind are specific but widespread in Firmicutes, where they originated. The present phylogenetic analyses brought to light a highly dynamic evolutionary history involving numerous horizontal gene transfers, duplications and lost events, leading to a great variety of Bce-like repertories in members of this bacterial phylum. Based on these phylogenetic analyses, it was proposed to subdivide the Bce-like modules into six well-defined subfamilies. Functional studies were performed on members of subfamily IV comprising BceRSAB from B. subtilis, the expression of which was found to require the signal transduction system as well as the ABC transporter itself. The present results suggest, for the members of this subfamily, the occurrence of interactions between one component of each partner, the kinase and the corresponding translocator. At functional and/or structural levels, bacitracin dependent expression of bceAB and bacitracin resistance processes require the presence of the BceB translocator loop. Some other members of subfamily IV were also found to participate in bacitracin resistance processes. Taken together our study suggests that this regulatory mechanism might constitute an important common antibiotic resistance mechanism in Firmicutes. [Supplemental material is available online at http://www.genome.org.].

Origin and diversification of TRIM ubiquitin ligases.

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Ignacio Marín

Full Text Available Most proteins of the TRIM family (also known as RBCC family are ubiquitin ligases that share a peculiar protein structure, characterized by including an N-terminal RING finger domain closely followed by one or two B-boxes. Additional protein domains found at their C termini have been used to classify TRIM proteins into classes. TRIMs are involved in multiple cellular processes and many of them are essential components of the innate immunity system of animal species. In humans, it has been shown that mutations in several TRIM-encoding genes lead to diverse genetic diseases and contribute to several types of cancer. They had been hitherto detected only in animals. In this work, by comprehensively analyzing the available diversity of TRIM and TRIM-like protein sequences and evaluating their evolutionary patterns, an improved classification of the TRIM family is obtained. Members of one of the TRIM subfamilies defined, called Subfamily A, turn to be present not only in animals, but also in many other eukaryotes, such as fungi, apusozoans, alveolates, excavates and plants. The rest of subfamilies are animal-specific and several of them originated only recently. Subfamily A proteins are characterized by containing a MATH domain, suggesting a potential evolutionary connection between TRIM proteins and a different type of ubiquitin ligases, known as TRAFs, which contain quite similar MATH domains. These results indicate that the TRIM family emerged much earlier than so far thought and contribute to our understanding of its origin and diversification. The structural and evolutionary links with the TRAF family of ubiquitin ligases can be experimentally explored to determine whether functional connections also exist.

Discovery of germacrene A synthases in Barnadesia spinosa: The first committed step in sesquiterpene lactone biosynthesis in the basal member of the Asteraceae.

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Nguyen, Trinh-Don; Faraldos, Juan A; Vardakou, Maria; Salmon, Melissa; O'Maille, Paul E; Ro, Dae-Kyun

2016-10-28

The Andes-endemic Barnadesioideae lineage is the oldest surviving and phylogenetically basal subfamily of the Asteraceae (Compositae), a prolific group of flowering plants with world-wide distribution (∼24,000 species) marked by a rich diversity of sesquiterpene lactones (STLs). Intriguingly, there is no evidence that members of the Barnadesioideae produce STLs, specialized metabolites thought to have contributed to the adaptive success of the Asteraceae family outside South America. The biosynthesis of STLs requires the intimate expression and functional integration of germacrene A synthase (GAS) and germacrene A oxidase (GAO) to sequentially cyclize and oxidize farnesyl diphosphate into the advanced intermediate germacrene A acid leading to diverse STLs. Our previous discovery of GAO activity conserved across all major subfamilies of Asteraceae, including the phylogenetically basal lineage of Barnadesioideae, prompted further investigation of the presence of the gateway GAS in Barnadesioideae. Herein we isolated two terpene synthases (BsGAS1/BsGAS2) from the basal Barnadesia spinosa (Barnadesioideae) that displayed robust GAS activity when reconstituted in yeast and characterized in vitro. Despite the apparent lack of STLs in the Barnadesioideae, this work unambiguously confirms the presence of GAS in the basal genera of the Asteraceae. Phylogenetic analysis reveals that the two BsGASs fall into two distinct clades of the Asteraceae's GASs, and BsGAS1 clade is only retained in the evolutionary closer Cichorioideae subfamily, implicating BsGAS2 is likely the ancestral base of most GASs found in the lineages outside the Barnadesioideae. Taken together, these results show the enzymatic capacities of GAS and GAO emerged prior to the subsequent radiation of STL-producing Asteraceae subfamilies. Copyright © 2016 Elsevier Inc. All rights reserved.

Meningococcal factor H-binding protein vaccines with decreased binding to human complement factor H have enhanced immunogenicity in human factor H transgenic mice.

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Rossi, Raffaella; Granoff, Dan M; Beernink, Peter T

2013-11-04

Factor H-binding protein (fHbp) is a component of a meningococcal vaccine recently licensed in Europe for prevention of serogroup B disease, and a second vaccine in clinical development. The protein specifically binds human factor H (fH), which down-regulates complement activation and enhances resistance to bactericidal activity. There are conflicting data from studies in human fH transgenic mice on whether binding of human fH to fHbp vaccines decreases immunogenicity, and whether mutant fHbp vaccines with decreased fH binding have enhanced immunogenicity. fHbp can be classified into two sub-families based on sequence divergence and immunologic cross-reactivity. Previous studies of mutant fHbp vaccines with low fH binding were from sub-family B, which account for approximately 60% of serogroup B case isolates. In the present study, we evaluated the immunogenicity of two mutant sub-family A fHbp vaccines containing single substitutions, T221A or D211A, which resulted in 15- or 30-fold lower affinity for human fH, respectively, than the corresponding control wild-type fHbp vaccine. In transgenic mice with high serum concentrations of human fH, both mutant vaccines elicited significantly higher IgG titers and higher serum bactericidal antibody responses than the control fHbp vaccine that bound human fH. Thus, mutations introduced into a sub-family A fHbp antigen to decrease fH binding can increase protective antibody responses in human fH transgenic mice. Collectively the data suggest that mutant fHbp antigens with decreased fH binding will result in superior vaccines in humans. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genome-wide identification and functional analysis of the TIFY gene family in response to drought in cotton.

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Zhao, Ge; Song, Yun; Wang, Caixiang; Butt, Hamama Islam; Wang, Qianhua; Zhang, Chaojun; Yang, Zuoren; Liu, Zhao; Chen, Eryong; Zhang, Xueyan; Li, Fuguang

2016-12-01

Jasmonates control many aspects of plant biological processes. They are important for regulating plant responses to various biotic and abiotic stresses, including drought, which is one of the most serious threats to sustainable agricultural production. However, little is known regarding how jasmonate ZIM-domain (JAZ) proteins mediate jasmonic acid signals to improve stress tolerance in cotton. This represents the first comprehensive comparative study of TIFY transcription factors in both diploid A, D and tetraploid AD cotton species. In this study, we identified 21 TIFY family members in the genome of Gossypium arboretum, 28 members from Gossypium raimondii and 50 TIFY genes in Gossypium hirsutum. The phylogenetic analyses indicated the TIFY gene family could be divided into the following four subfamilies: TIFY, PPD, ZML, and JAZ subfamilies. The cotton TIFY genes have expanded through tandem duplications and segmental duplications compared with other plant species. Gene expression profile revealed temporal and tissue specificities for TIFY genes under simulated drought conditions in Gossypium arboretum. The JAZ subfamily members were the most highly expressed genes, suggesting that they have a vital role in responses to drought stress. Over-expression of GaJAZ5 gene decreased water loss, stomatal openings, and the accumulation of H 2 O 2 in Arabidopsis thaliana. Additionally, the results of drought tolerance assays suggested that this subfamily might be involved in increasing drought tolerance. Our study provides new data regarding the genome-wide analysis of TIFY gene families and their important roles in drought tolerance in cotton species. These data may form the basis of future studies regarding the relationship between drought and jasmonic acid.

New fossil ants in French Cretaceous amber (Hymenoptera: Formicidae)

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Perrichot, Vincent; Nel, André; Néraudeau, Didier; Lacau, Sébastien; Guyot, Thierry

2008-02-01

Recent studies on the ant phylogeny are mainly based on the molecular analyses of extant subfamilies and do not include the extinct, only Cretaceous subfamily Sphecomyrminae. However, the latter is of major importance for ant relationships, as it is considered the most basal subfamily. Therefore, each new discovery of a Mesozoic ant is of high interest for improving our understanding of their early history and basal relationships. In this paper, a new sphecomyrmine ant, allied to the Burmese amber genus Haidomyrmex, is described from mid-Cretaceous amber of France as Haidomyrmodes mammuthus gen. and sp. n. The diagnosis of the tribe Haidomyrmecini is emended based on the new type material, which includes a gyne (alate female) and two incomplete workers. The genus Sphecomyrmodes, hitherto known by a single species from Burmese amber, is also reported and a new species described as S. occidentalis sp. n. after two workers remarkably preserved in a single piece of Early Cenomanian French amber. The new fossils provide additional information on early ant diversity and relationships and demonstrate that the monophyly of the Sphecomyrminae, as currently defined, is still weakly supported.

The Representatives of Amelanchier Medik. Genus in Ukraine

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Opalko Anatoliy Ivanovich

2015-04-01

Full Text Available The information on fruit and decorative value, honey and medicinal properties of the genus Amelanchier Medik. is generalized. Their biological characteristics, chemical composition and palatability traits of the fruit, the ways of consumption and processing, including drying, preparing juices, syrups, jams, candied fruit jellies, confiture, and fruit wine are specified. The environmental adaptability and effectiveness of using juneberry for phytomelioration are mentioned. Several versions of the origin of the genus Amelanchier name and interpretation of its specific epithets are described. The controversial issues of the genus Amelanchier system were discussed from the classical and molecular genetic approaches. The attention is focused on two main aspects of views on the place of the genus Amelanchier representatives of the family Rosaceae Juss. within the particular subfamily, namely the subfamily Pyroideae Burnett (Maloideae S. Weber or the subfamily Amygdaloideae Arn., which indicates the necessity for further comparative morphological and molecular genetic studies of the family Rosaceae. The directions of evolution, habitat and invasive ability of some species of the genus Amelanchier are characterised. The list of the genus Amelanchier representatives cultivated in Ukraine is given.

Co-localisation studies of Arabidopsis SR splicing factors reveal different types of speckles in plant cell nuclei

International Nuclear Information System (INIS)

Lorkovic, Zdravko J.; Hilscher, Julia; Barta, Andrea

2008-01-01

SR proteins are multidomain splicing factors which are important for spliceosome assembly and for regulation of alternative splicing. In mammalian nuclei these proteins localise to speckles from where they are recruited to transcription sites. By using fluorescent protein fusion technology and different experimental approaches it has been shown that Arabidopsis SR proteins, in addition to diffuse nucleoplasmic staining, localise into an irregular nucleoplasmic network resembling speckles in mammalian cells. As Arabidopsis SR proteins fall into seven conserved sub-families we investigated co-localisation of members of the different sub-families in transiently transformed tobacco protoplast. Here we demonstrate the new finding that members of different SR protein sub-families localise into distinct populations of nuclear speckles with no, partial or complete co-localisation. This is particularly interesting as we also show that these proteins do interact in a yeast two-hybrid assay as well as in pull-down and in co-immunopreciptiation assays. Our data raise the interesting possibility that SR proteins are partitioned into distinct populations of nuclear speckles to allow a more specific recruitment to the transcription/pre-mRNA processing sites of particular genes depending on cell type and developmental stage

IL-22R Ligands IL-20, IL-22, and IL-24 Promote Wound Healing in Diabetic db/db Mice.

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Kolumam, Ganesh; Wu, Xiumin; Lee, Wyne P; Hackney, Jason A; Zavala-Solorio, Jose; Gandham, Vineela; Danilenko, Dimitry M; Arora, Puneet; Wang, Xiaoting; Ouyang, Wenjun

2017-01-01

Diabetic foot ulcers (DFU) are one of the major complications in type II diabetes patients and can result in amputation and morbidity. Although multiple approaches are used clinically to help wound closure, many patients still lack adequate treatment. Here we show that IL-20 subfamily cytokines are upregulated during normal wound healing. While there is a redundant role for each individual cytokine in this subfamily in wound healing, mice deficient in IL-22R, the common receptor chain for IL-20, IL-22, and IL-24, display a significant delay in wound healing. Furthermore, IL-20, IL-22 and IL-24 are all able to promote wound healing in type II diabetic db/db mice. Mechanistically, when compared to other growth factors such as VEGF and PDGF that accelerate wound healing in this model, IL-22 uniquely induced genes involved in reepithelialization, tissue remodeling and innate host defense mechanisms from wounded skin. Interestingly, IL-22 treatment showed superior efficacy compared to PDGF or VEGF in an infectious diabetic wound model. Taken together, our data suggest that IL-20 subfamily cytokines, particularly IL-20, IL-22, and IL-24, might provide therapeutic benefit for patients with DFU.

Morphological characters are compatible with mitogenomic data in resolving the phylogeny of nymphalid butterflies (lepidoptera: papilionoidea: nymphalidae).

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Shi, Qing-Hui; Sun, Xiao-Yan; Wang, Yun-Liang; Hao, Jia-Sheng; Yang, Qun

2015-01-01

Nymphalidae is the largest family of butterflies with their phylogenetic relationships not adequately approached to date. The mitochondrial genomes (mitogenomes) of 11 new nymphalid species were reported and a comparative mitogenomic analysis was conducted together with other 22 available nymphalid mitogenomes. A phylogenetic analysis of the 33 species from all 13 currently recognized nymphalid subfamilies was done based on the mitogenomic data set with three Lycaenidae species as the outgroups. The mitogenome comparison showed that the eleven new mitogenomes were similar with those of other butterflies in gene content and order. The reconstructed phylogenetic trees reveal that the nymphalids are made up of five major clades (the nymphaline, heliconiine, satyrine, danaine and libytheine clades), with sister relationship between subfamilies Cyrestinae and Biblidinae, and most likely between subfamilies Morphinae and Satyrinae. This whole mitogenome-based phylogeny is generally congruent with those of former studies based on nuclear-gene and mitogenomic analyses, but differs considerably from the result of morphological cladistic analysis, such as the basal position of Libytheinae in morpho-phylogeny is not confirmed in molecular studies. However, we found that the mitogenomic phylogeny established herein is compatible with selected morphological characters (including developmental and adult morpho-characters).

Functional Diversity of Fibroblast Growth Factors in Bone Formation

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Yuichiro Takei

2015-01-01

Full Text Available The functional significance of fibroblast growth factor (FGF signaling in bone formation has been demonstrated through genetic loss-of-function and gain-of-function approaches. FGFs, comprising 22 family members, are classified into three subfamilies: canonical, hormone-like, and intracellular. The former two subfamilies activate their signaling pathways through FGF receptors (FGFRs. Currently, intracellular FGFs appear to be primarily involved in the nervous system. Canonical FGFs such as FGF2 play significant roles in bone formation, and precise spatiotemporal control of FGFs and FGFRs at the transcriptional and posttranscriptional levels may allow for the functional diversity of FGFs during bone formation. Recently, several research groups, including ours, have shown that FGF23, a member of the hormone-like FGF subfamily, is primarily expressed in osteocytes/osteoblasts. This polypeptide decreases serum phosphate levels by inhibiting renal phosphate reabsorption and vitamin D3 activation, resulting in mineralization defects in the bone. Thus, FGFs are involved in the positive and negative regulation of bone formation. In this review, we focus on the reciprocal roles of FGFs in bone formation in relation to their local versus systemic effects.

A chromosomal analysis of four species of Chilean Chrysomelinae (Coleoptera, Chrysomelidae

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Eduard Petitpierre

2012-10-01

Full Text Available Four species of Chilean leaf beetles in the subfamily Chrysomelinae have been cytogenetically analyzed, Blaptea elguetai Petitpierre, 2011, Henicotherus porteri Bréthes, 1929 and Jolivetia obscura (Philippi, 1864 show 2n = 28 chromosomes and a 13 + Xyp male meioformula, and Pataya nitida (Philippi, 1864 has the highest number of 2n = 38 chromosomes. The karyotype of H. porteri is made of mostly small meta/submetacentric chromosomes, and that of Jolivetia obscura displays striking procentric blocks of heterochromatin at pachytene autosomic bivalents using conventional staining. These findings are discussed in relation to previous cytogenetic data and current taxonomy of the subfamily.

A chromosomal analysis of four species of Chilean Chrysomelinae (Coleoptera, Chrysomelidae)

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Petitpierre, Eduard; Elgueta, Mario

2012-01-01

Abstract Four species of Chilean leaf beetles in the subfamily Chrysomelinae have been cytogenetically analyzed, Blaptea elguetai Petitpierre, 2011, Henicotherus porteri Bréthes, 1929 and Jolivetia obscura (Philippi, 1864) show 2n = 28 chromosomes and a 13 + Xyp male meioformula, and Pataya nitida (Philippi, 1864) has the highest number of 2n = 38 chromosomes. The karyotype of Henicotherus porteri is made of mostly small meta/submetacentric chromosomes, and that of Jolivetia obscura displays striking procentric blocks of heterochromatin at pachytene autosomic bivalents using conventional staining. These findings are discussed in relation to previous cytogenetic data and current taxonomy of the subfamily. PMID:24260673

Molecular phylogeny of microhylid frogs (Anura: Microhylidae with emphasis on relationships among New World genera

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de Sá Rafael O

2012-12-01

Full Text Available Abstract Background Over the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e., incertae sedis. Results One mitochondrial and three nuclear genes (about 2.8 kb were sequenced to assess phylogenetic relationships. We utilized an unprecedented sampling of 200 microhylid taxa representing 91% of currently recognized subfamilies and 95% of New World genera. Our analyses do not fully resolve relationships among subfamilies supporting previous studies that have suggested a rapid early diversification of this clade. We observed a close relationship between Synapturanus and Otophryne of the subfamily Otophryninae. Within the subfamily Gastrophryninae relationships between genera were well resolved. Conclusion Otophryninae is distantly related to all other New World microhylids that were recovered as a monophyletic group, Gastrophryninae. Within Gastrophryninae, five genera were recovered as non-monophyletic; we propose taxonomic re-arrangements to render all genera monophyletic. This hypothesis of relationships and updated classification for New World microhylids may serve as a guide to better understand the evolutionary history of this group that is apparently subject to convergent morphological evolution and chromosome reduction. Based on a divergence analysis calibrated with hypotheses from previous studies and fossil data, it appears that microhylid genera inhabiting the New World originated during a period of gradual cooling from the late Oligocene to

Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes.

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Steppan, Scott; Adkins, Ronald; Anderson, Joel

2004-08-01

The muroid rodents are the largest superfamily of mammals, containing nearly one third of all mammal species. We report on a phylogenetic study comprising 53 genera sequenced for four nuclear genes, GHR, BRCA1, RAG1, and c-myc, totaling up to 6400 nucleotides. Most relationships among the subfamilies are resolved. All four genes yield nearly identical phylogenies, differing only in five key regions, four of which may represent particularly rapid radiations. Support is very strong for a fundamental division of the mole rats of the subfamilies Spalacinae and Rhizomyinae from all other muroids. Among the other "core" muroids, a rapid radiation led to at least four distinct lineages: Asian Calomyscus, an African clade of at least four endemic subfamilies, including the diverse Nesomyinae of Madagascar, a hamster clade with maximum diversity in the New World, and an Old World clade including gerbils and the diverse Old World mice and rats (Murinae). The Deomyinae, recently removed from the Murinae, is well supported as the sister group to the gerbils (Gerbillinae). Four key regions appear to represent rapid radiations and, despite a large amount of sequence data, remain poorly resolved: the base of the "core" muroids, among the five cricetid (hamster) subfamilies, within a large clade of Sigmodontinae endemic to South America, and among major geographic lineages of Old World Murinae. Because of the detailed taxon sampling within the Murinae, we are able to refine the fossil calibration of a rate-smoothed molecular clock and apply this clock to date key events in muroid evolution. We calculate rate differences among the gene regions and relate those differences to relative contribution of each gene to the support for various nodes. The among-gene variance in support is greatest for the shortest branches. We present a revised classification for this largest but most unsettled mammalian superfamily.

The Enterobiinae subfam. Nov. (Nematoda, Oxyurida) pinworm parasites of primates and rodents.

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Hugot, J P; Gardner, S L; Morand, S

1996-02-01

Recent redescriptions of most members of the Oxyuridae Cobbold, 1864 parasitic in primates revealed that they share following derived characters: sexual dimorphism of lateral alae (single-crested in the males, double-crested in the females); in males a second pair of genital papillae always surrounded by strongly cuticularized rings; in females, uterine tube divided into 2 parts by a cellular wall forming a diaphragm. These characters are interpreted as synapomorphies, providing evidence that these taxa represent a monophyletic group, and we propose to classify them in a new subfamily of the Oxyuridae: the Enterobiinae subfam.nov. The Enterobiinae as recognized herein occurs in both Old World and New World Primates and rodents of the family Sciuridae (tribe Sciurini in the Holarctic region and tribe Xerini in the Ethiopian region). The new subfamily includes the following genera: Enterobius Leach, 1853; Colobenterobius Quentin, Betterton & Krishnasamy, 1979; Rodentoxyuris Quentin & Tenora 1974; Xeroxyuris Hugot, 1995; Lemuricola Chabaud & Petter, 1959; Protenterobius Inglis, 1961; Madoxyuris Chabaud, Brygoo & Petter, 1965; Trypanoxyuris Vevers, 1923; Hapaloxyuris Inglis & Cosgrove, 1965 and Paraoxyuronema Artigas, 1936. The genus Paraoxyuronema is revalidated as a subgenus of Trypanoxyuris due to its specialized buccal structures. This genus groups all pinworm nematodes specific for primates of the family Atelidae, including: P. brachytelesi Artigas, 1937 occurring in Brachyteles arachnoides; P. atelis (Cameron, 1929) occurring in Ateles spp., and P. duplicidens (Buckley, 1931) and P. lagothricis (Buckley, 1931), which are parasites of Lagothrix spp. Inglisoxyuris inglisi Chabaud, Petter & Golvan, 1961, included in the monospecific genus Inglisoxyuris and previously classified as a subgenus of the Lemuricola, does not share the characters of the new subfamily and, until its precise classification can be considered with more information, it is proposed to refer to

Molecular systematic and historical biogeography of the armored Neotropical catfishes Hypoptopomatinae and Neoplecostominae (Siluriformes: Loricariidae).

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Chiachio, Márcio Cesar; Oliveira, Claudio; Montoya-Burgos, Juan I

2008-11-01

The Neotropics possess the greatest freshwater fish diversity of the world, rendering the study of their evolutionary history extremely challenging. Loricariidae catfishes are one of the most diverse components of the Neotropical ichthyofauna and despite a long history of classification, major issues still need elucidation. Based on a nuclear gene, we present a robust phylogeny of two former loricariid subfamilies: Hypoptopomatinae and Neoplecostominae. Our results show that Neoplecostominae is nested within Hypoptopomatinae, and is the sister group to the former Otothyrini tribe. According to our results, supplemented by morphological observations, we erect two new subfamilies, the Otothyrinae and a new Hypoptopomatinae, and modify the Neoplecostominae by including the genus Pseudotocinclus. The uncovered evolutionary relationships allow a detailed analysis of their historical biogeography. We tested two Dispersal-Extinction-Cladogenesis models for inferring the distribution range evolution of the new subfamilies, and show that the model having no constrains performs better than a model constraining long-range dispersal. The Maximum Likelihood reconstructions of ancestral ranges showed a marked division between the Amazonian origin of the Hypoptopomatinae and the eastern coastal Brazil+Upper Paraná origin of the Neoplecostominae and Otothyrinae. Markedly few instances of dispersal across the border separating the Amazon basin and the Paraná-Paraguay+eastern coastal Brazil+Uruguay were reconstructed. This result is in clear contrast with the historical biogeography of many Neotropical fishes, including other Loricariidae. Part of the dispersal limitation may be explained by divergent ecological specialization: lowland rivers versus mountain streams habitats. Moreover, because most species of the new subfamilies are small, we hypothesize that body size-related effects might limit their dispersal, like predation and energetic cost to migration. Finally

Fossil Bovidae from the Malay Archipelago and the Punjab

NARCIS (Netherlands)

Hooijer, D.A.

1958-01-01

CONTENTS Introduction................... 1 Order Artiodactyla Owen............... 8 Family Bovidae Gray................ 8 Subfamily Bovinae Gill................ 8 Duboisia santeng (Dubois).............. 8 Epileptobos groeneveldtii (Dubois)............ 19 Hemibos triquetricornis Rütimeyer............

Genome-wide comparative analysis of papain-like cysteine protease family genes in castor bean and physic nut.

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Zou, Zhi; Huang, Qixing; Xie, Guishui; Yang, Lifu

2018-01-10

Papain-like cysteine proteases (PLCPs) are a class of proteolytic enzymes involved in many plant processes. Compared with the extensive research in Arabidopsis thaliana, little is known in castor bean (Ricinus communis) and physic nut (Jatropha curcas), two Euphorbiaceous plants without any recent whole-genome duplication. In this study, a total of 26 or 23 PLCP genes were identified from the genomes of castor bean and physic nut respectively, which can be divided into nine subfamilies based on the phylogenetic analysis: RD21, CEP, XCP, XBCP3, THI, SAG12, RD19, ALP and CTB. Although most of them harbor orthologs in Arabidopsis, several members in subfamilies RD21, CEP, XBCP3 and SAG12 form new groups or subgroups as observed in other species, suggesting specific gene loss occurred in Arabidopsis. Recent gene duplicates were also identified in these two species, but they are limited to the SAG12 subfamily and were all derived from local duplication. Expression profiling revealed diverse patterns of different family members over various tissues. Furthermore, the evolution characteristics of PLCP genes were also compared and discussed. Our findings provide a useful reference to characterize PLCP genes and investigate the family evolution in Euphorbiaceae and species beyond.

Nuclear and cpDNA sequences combined provide strong inference of higher phylogenetic relationships in the phlox family (Polemoniaceae).

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Johnson, Leigh A; Chan, Lauren M; Weese, Terri L; Busby, Lisa D; McMurry, Samuel

2008-09-01

Members of the phlox family (Polemoniaceae) serve as useful models for studying various evolutionary and biological processes. Despite its biological importance, no family-wide phylogenetic estimate based on multiple DNA regions with complete generic sampling is available. Here, we analyze one nuclear and five chloroplast DNA sequence regions (nuclear ITS, chloroplast matK, trnL intron plus trnL-trnF intergeneric spacer, and the trnS-trnG, trnD-trnT, and psbM-trnD intergenic spacers) using parsimony and Bayesian methods, as well as assessments of congruence and long branch attraction, to explore phylogenetic relationships among 84 ingroup species representing all currently recognized Polemoniaceae genera. Relationships inferred from the ITS and concatenated chloroplast regions are similar overall. A combined analysis provides strong support for the monophyly of Polemoniaceae and subfamilies Acanthogilioideae, Cobaeoideae, and Polemonioideae. Relationships among subfamilies, and thus for the precise root of Polemoniaceae, remain poorly supported. Within the largest subfamily, Polemonioideae, four clades corresponding to tribes Polemonieae, Phlocideae, Gilieae, and Loeselieae receive strong support. The monogeneric Polemonieae appears sister to Phlocideae. Relationships within Polemonieae, Phlocideae, and Gilieae are mostly consistent between analyses and data permutations. Many relationships within Loeselieae remain uncertain. Overall, inferred phylogenetic relationships support a higher-level classification for Polemoniaceae proposed in 2000.

Genome-Wide Identification and Characterization of Tyrosine Kinases in the Silkworm, Bombyx mori

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Songzhen He

2018-03-01

Full Text Available The tyrosine kinases (TKs are important parts of metazoan signaling pathways and play significant roles in cell growth, development, apoptosis and disease. Genome-wide characterization of TKs has been conducted in many metazoans, however, systematic information about this family in Lepidoptera is still lacking. We retrieved 33 TK-encoding genes in silkworm and classified them into 25 subfamilies by sequence analysis, without members in AXL, FRK, PDGFR, STYK1 and TIE subfamilies. Although domain sequences in each subfamily are conserved, TKs in vertebrates tend to be remarkably conserved and stable. Our results of phylogenetic analysis supported the previous conclusion for the second major expansion of TK family. Gene-Ontology (GO analysis revealed that a higher proportion of BmTKs played roles in binding, catalysis, signal transduction, metabolism, biological regulation and response to stimulus, compared to all silkworm genes annotated in GO. Moreover, the expression profile analysis of BmTKs among multiple tissues and developmental stages demonstrated that many genes exhibited stage-specific and/or sex-related expression during embryogenesis, molting and metamorphosis, and that 8 BmTKs presented tissue-specific high expression. Our study provides systematic description of silkworm tyrosine kinases, and may also provide further insights into metazoan TKs and assist future studies addressing their functions.

The function and evolution of Wnt genes in arthropods.

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Murat, Sophie; Hopfen, Corinna; McGregor, Alistair P

2010-11-01

Wnt signalling is required for a wide range of developmental processes, from cleavage to patterning and cell migration. There are 13 subfamilies of Wnt ligand genes and this diverse repertoire appeared very early in metazoan evolution. In this review, we first summarise the known Wnt gene repertoire in various arthropods. Insects appear to have lost several Wnt subfamilies, either generally, such as Wnt3, or in lineage specific patterns, for example, the loss of Wnt7 in Anopheles. In Drosophila and Acyrthosiphon, only seven and six Wnt subfamilies are represented, respectively; however, the finding of nine Wnt genes in Tribolium suggests that arthropods had a larger repertoire ancestrally. We then discuss what is currently known about the expression and developmental function of Wnt ligands in Drosophila and other insects in comparison to other arthropods, such as the spiders Achaearanea and Cupiennius. We conclude that studies of Wnt genes have given us much insight into the developmental roles of some of these ligands. However, given the frequent loss of Wnt genes in insects and the derived development of Drosophila, further studies of these important genes are required in a broader range of arthropods to fully understand their developmental function and evolution. Copyright © 2010 Elsevier Ltd. All rights reserved.

Diversity of canopy ants at a reserve area of Prince of Songkla University, Songkhla

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Takodee, T.

2007-03-01

Full Text Available Diversity of canopy ants was examined by using pyrethoid fogging technique at a reserve area of Prince of Songkla University, Songkhla Province. A permanent plot of 100x100 m2 was set up and dividedinto 100 sub-units (10x10 m2. Three plants were randomly selected for pyrethoid fogging applications each time bimothly during July 2004 - May 2005. The results showed that a total of 2,343 individuals were collectedin 14 genera, 5 subfamily and 31 species. The Formicinae and Myrmicinae were the major subfamilies found in equal species numbers of 13. Shannon- Weiner Index and evenness value of ants were 1.73±0.39 and 0.35±0.08, respectively.Seasonal changes (wet and dry had no effect on individual numbers of ant species in each subfamily. The influence of physical factors (rainfall, temperature and relative humidity on numbers of ant species wasalso investigated. A significant negative correlation between rainfall and species numbers of Camponotus (Tanaemyrmex sp.2 was found, while temperature had a significant positive correlation with Crematogaster (Orthocrema sp.4, Meranoplus castaneus (F.Smith and Tetraponera sp.4, and relative humidity had asignificant positive correlation with only Tetraponera sp.4.

Structural and biochemical analysis of atypically low dephosphorylating activity of human dual-specificity phosphatase 28.

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Bonsu Ku

Full Text Available Dual-specificity phosphatases (DUSPs constitute a subfamily of protein tyrosine phosphatases, and are intimately involved in the regulation of diverse parameters of cellular signaling and essential biological processes. DUSP28 is one of the DUSP subfamily members that is known to be implicated in the progression of hepatocellular and pancreatic cancers, and its biological functions and enzymatic characteristics are mostly unknown. Herein, we present the crystal structure of human DUSP28 determined to 2.1 Å resolution. DUSP28 adopts a typical DUSP fold, which is composed of a central β-sheet covered by α-helices on both sides and contains a well-ordered activation loop, as do other enzymatically active DUSP proteins. The catalytic pocket of DUSP28, however, appears hardly accessible to a substrate because of the presence of nonconserved bulky residues in the protein tyrosine phosphatase signature motif. Accordingly, DUSP28 showed an atypically low phosphatase activity in the biochemical assay, which was remarkably improved by mutations of two nonconserved residues in the activation loop. Overall, this work reports the structural and biochemical basis for understanding a putative oncological therapeutic target, DUSP28, and also provides a unique mechanism for the regulation of enzymatic activity in the DUSP subfamily proteins.

Genome inventory and analysis of nuclear hormone receptors in ...

Indian Academy of Sciences (India)

Prakash

2006-12-20

Dec 20, 2006 ... progestins, as well as lipids, cholesterol metabolites, and. Genome ... Gene structure analysis shows strong conservation of exon structures among orthologoues. ..... earlier subfamily classification of NRs (Nuclear Receptors.

Braconidae (Hymenoptera fauna in native, degraded and restoration areas of the Vale do Paraíba, São Paulo state, Brazil

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CA Barbieri Junior

Full Text Available This study sampled the diversity of Braconidae (Hymenoptera in three different ecosystems: a degraded pasture, a secondary forest and an area in recovery process using native tree seedlings. The objective was to verify the use of those insects as a tool to check the local conservation by examining Shannon's diversity index. Ten subfamilies were identified, and Microgastrinae was predominant in a number of individuals. The diversity index calculated varies among the sampled areas, thus showing a correlation with vegetation cover with the number of individuals collected and number of subfamilies found. The results showed changes in the community of Braconidae, in the recovery area between the first and second year of study, thereby leading to the conclusion that they are indicators of environmental quality.

Cloning and molecular characterization of the salt-regulated jojoba ScRab cDNA encoding a small GTP-binding protein.

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Mizrahi-Aviv, Ela; Mills, David; Benzioni, Aliza; Bar-Zvi, Dudy

2002-10-01

Salt stress results in a massive change in gene expression. An 837 bp cDNA designated ScRab was cloned from shoot cultures of the salt tolerant jojoba (Simmondsia chinesis). The cloned cDNA encodes a full length 200 amino acid long polypeptide that bears high homology to the Rab subfamily of small GTP binding proteins, particularly, the Rab5 subfamily. ScRab expression is reduced in shoots grown in the presence of salt compared to shoots from non-stressed cultures. His6-tagged ScRAB protein was expressed in E. coli, and purified to homogeneity. The purified protein bound radiolabelled GTP. The unlabelled guanine nucleotides GTP, GTP gamma S and GDP but not ATP, CTP or UTP competed with GTP binding.

Cerambycidae (Coleoptera from Lagoa do Tamburí farm, Aracatu – Bahia, with new records

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ANDRÉ DA SILVA FERREIRA

2015-01-01

Full Text Available ABSTRACTSpecies of Cerambycidae were inventoried in an area of Caatinga (dryland vegetation in the municipality of Aracatu, Bahia State, Brazil, between August/2012 and July/2013. The insects were collected using light traps, active searches, and white cloth trapping. A total of 716 specimens of Cerambycidae were collected; 665 of them were identified as belonging to 107 species, 84 genera, 30 tribes, and 3 subfamilies. The speciesPhaedinus carbonelli Monné, 1999,Lepturges (Lepturges fasciculatoides Gilmour, 1962,Hoplistonychus bondari Melzer, 1930,Ataxia arenaria Martins & Galileo, 2013 were new records for Bahia;Nesozineus obscurus Hoffmann, 1984 is new record for Brazil. The subfamily Cerambycinae demonstrated the greatest richness, with 56 species. These results contribute to our knowledge of the Cerambycidae fauna of Brazil.

Ophioninae (Hymenoptera: Ichneumonidae wasp community in the cloudy forest Monteseco, Cajamarca, Peru

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Evelyn Sánchez

2014-12-01

Full Text Available We describe the species composition of the subfamily Ophioninae (Hymenoptera: Ichneumonidae along an altitudinal gradient in the cloudy forest Monteseco, Cajamarca, Peru collected in 2009 and 2010. Eighteen species were recorded in three genera of Ophioninae: Alophophion, Enicospilus y Ophion. Five species are recorded for the first time in Peru: Ophion polyhymniae Gauld, 1988; Enicospilus cubensis (Norton, 1863; E. guatemalensis (Cameron, 1886; E. cressoni Hooker, 1912 y E. mexicanus (Cresson, 1874. Subfamily composition varies with the elevation. The highest species richness (S=11 was found at 2150 m and the lowest (S=3 at 3116 m. Enicospilus is more diverse from low to mid elevation, Ophion from mid to high elevation and Alophophion occurs predominantly at high elevation.

Expression and regulation of prostaglandin transporters, ATP-binding cassette, subfamily C, member 1 and 9, and solute carrier organic anion transporter family, member 2A1 and 5A1 in the uterine endometrium during the estrous cycle and pregnancy in pigs

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Hwanhee Jang

2017-05-01

Full Text Available Objective Prostaglandins (PGs function in various reproductive processes, including luteolysis, maternal pregnancy recognition, conceptus development, and parturition. Our earlier study has shown that PG transporters ATP-binding cassette, subfamily C, member 4 (ABCC4 and solute carrier organic anion transporter family, member 2A1 (SLCO2A1 are expressed in the uterine endometrium in pigs. Since several other PG transporters such as ABCC1, ABCC9, SLCO4C1, and SLCO5A1 are known to be present in the uterine endometrium, this study investigated the expression of these PG transporters in the porcine uterine endometrium and placenta. Methods Uterine endometrial tissues were obtained from gilts on day (D 12 and D15 of the estrous cycle and days 12, 15, 30, 60, 90, and 114 of pregnancy. Results ABCC1, ABCC9, SLCO4C1, and SLCO5A1 mRNAs were expressed in the uterine endometrium, and levels of expression changed during the estrous cycle and pregnancy. Expression of ABCC1 and ABCC9 mRNAs was localized mainly to luminal and glandular epithelial cells in the uterine endometrium, and chorionic epithelial cells during pregnancy. Conceptuses during early pregnancy and chorioallantoic tissues from mid to late pregnancy also expressed these PG transporters. Estradiol-17β increased the expression of ABCC1 and SLCO5A1, but not ABCC9 and SLCO4C1 mRNAs and increasing doses of interleukin-1β induced the expression of ABCC9, SLCO4C1, and SLCO5A1 mRNAs in endometrial explant tissues. Conclusion These data showed that several PG transporters such as ABCC1, ABCC9, SLCO4C1, and SLCO5A1 were expressed at the maternal-conceptus interface, suggesting that these PG transporters may play an important role in the establishment and maintenance of pregnancy by regulating PG transport in the uterine endometrium and placenta in pigs.

Identification of a novel bile acid in swans, tree ducks, and geese: 3alpha,7alpha,15alpha-trihydroxy-5beta-cholan-24-oic acid.

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Kakiyama, Genta; Iida, Takashi; Goto, Takaaki; Mano, Nariyasu; Goto, Junichi; Nambara, Toshio; Hagey, Lee R; Schteingart, Claudio D; Hofmann, Alan F

2006-07-01

By HPLC, a taurine-conjugated bile acid with a retention time different from that of taurocholate was found to be present in the bile of the black-necked swan, Cygnus melanocoryphus. The bile acid was isolated and its structure, established by (1)H and (13)C NMR and mass spectrometry, was that of the taurine N-acyl amidate of 3alpha,7alpha,15alpha-trihydroxy-5beta-cholan-24-oic acid. The compound was shown to have chromatographic and spectroscopic properties that were identical to those of the taurine conjugate of authentic 3alpha,7alpha,15alpha-trihydroxy-5beta-cholan-24-oic acid, previously synthesized by us from ursodeoxycholic acid. By HPLC, the taurine conjugate of 3alpha,7alpha,15alpha-trihydroxy-5beta-cholan-24-oic acid was found to be present in 6 of 6 species in the subfamily Dendrocygninae (tree ducks) and in 10 of 13 species in the subfamily Anserinae (swans and geese) but not in other subfamilies in the Anatidae family. It was also not present in species from the other two families of the order Anseriformes. 3alpha,7alpha,15alpha-Trihydroxy-5beta-cholan-24-oic acid is a new primary bile acid that is present in the biliary bile acids of swans, tree ducks, and geese and may be termed 15alpha-hydroxy-chenodeoxycholic acid.

Comparative analyses of lipoprotein lipase, hepatic lipase, and endothelial lipase, and their binding properties with known inhibitors.

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Ziyun Wang

Full Text Available The triglyceride lipase gene subfamily plays a central role in lipid and lipoprotein metabolism. There are three members of this subfamily: lipoprotein lipase, hepatic lipase, and endothelial lipase. Although these lipases are implicated in the pathophysiology of hyperlipidemia and atherosclerosis, their structures have not been fully solved. In the current study, we established homology models of these three lipases, and carried out analysis of their activity sites. In addition, we investigated the kinetic characteristics for the catalytic residues using a molecular dynamics simulation strategy. To elucidate the molecular interactions and determine potential key residues involved in the binding to lipase inhibitors, we analyzed the binding pockets and binding poses of known inhibitors of the three lipases. We identified the spatial consensus catalytic triad "Ser-Asp-His", a characteristic motif in all three lipases. Furthermore, we found that the spatial characteristics of the binding pockets of the lipase molecules play a key role in ligand recognition, binding poses, and affinities. To the best of our knowledge, this is the first report that systematically builds homology models of all the triglyceride lipase gene subfamily members. Our data provide novel insights into the molecular structures of lipases and their structure-function relationship, and thus provides groundwork for functional probe design towards lipase-based therapeutic inhibitors for the treatment of hyperlipidemia and atherosclerosis.

The Plasmodium serine-type SERA proteases display distinct expression patterns and non-essential in vivo roles during life cycle progression of the malaria parasite.

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Putrianti, Elyzana D; Schmidt-Christensen, Anja; Arnold, Iris; Heussler, Volker T; Matuschewski, Kai; Silvie, Olivier

2010-06-01

Parasite proteases play key roles in several fundamental steps of the Plasmodium life cycle, including haemoglobin degradation, host cell invasion and parasite egress. Plasmodium exit from infected host cells appears to be mediated by a class of papain-like cysteine proteases called 'serine repeat antigens' (SERAs). A SERA subfamily, represented by Plasmodium falciparum SERA5, contains an atypical active site serine residue instead of a catalytic cysteine. Members of this SERAser subfamily are abundantly expressed in asexual blood stages, rendering them attractive drug and vaccine targets. In this study, we show by antibody localization and in vivo fluorescent tagging with the red fluorescent protein mCherry that the two P. berghei serine-type family members, PbSERA1 and PbSERA2, display differential expression towards the final stages of merozoite formation. Via targeted gene replacement, we generated single and double gene knockouts of the P. berghei SERAser genes. These loss-of-function lines progressed normally through the parasite life cycle, suggesting a specialized, non-vital role for serine-type SERAs in vivo. Parasites lacking PbSERAser showed increased expression of the cysteine-type PbSERA3. Compensatory mechanisms between distinct SERA subfamilies may thus explain the absence of phenotypical defect in SERAser disruptants, and challenge the suitability to develop potent antimalarial drugs based on specific inhibitors of Plasmodium serine-type SERAs.

Improved phylogenetic analyses corroborate a plausible position of Martialis heureka in the ant tree of life.

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Patrick Kück

Full Text Available Martialinae are pale, eyeless and probably hypogaeic predatory ants. Morphological character sets suggest a close relationship to the ant subfamily Leptanillinae. Recent analyses based on molecular sequence data suggest that Martialinae are the sister group to all extant ants. However, by comparing molecular studies and different reconstruction methods, the position of Martialinae remains ambiguous. While this sister group relationship was well supported by Bayesian partitioned analyses, Maximum Likelihood approaches could not unequivocally resolve the position of Martialinae. By re-analysing a previous published molecular data set, we show that the Maximum Likelihood approach is highly appropriate to resolve deep ant relationships, especially between Leptanillinae, Martialinae and the remaining ant subfamilies. Based on improved alignments, alignment masking, and tree reconstructions with a sufficient number of bootstrap replicates, our results strongly reject a placement of Martialinae at the first split within the ant tree of life. Instead, we suggest that Leptanillinae are a sister group to all other extant ant subfamilies, whereas Martialinae branch off as a second lineage. This assumption is backed by approximately unbiased (AU tests, additional Bayesian analyses and split networks. Our results demonstrate clear effects of improved alignment approaches, alignment masking and data partitioning. We hope that our study illustrates the importance of thorough, comprehensible phylogenetic analyses using the example of ant relationships.

Genome-wide identification of whole ATP-binding cassette (ABC) transporters in the intertidal copepod Tigriopus japonicus.

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Jeong, Chang-Bum; Kim, Bo-Mi; Lee, Jae-Seong; Rhee, Jae-Sung

2014-08-05

The ATP-binding cassette (ABC) transporter superfamily is one of the largest transporter gene families and is observed in all animal taxa. Although a large set of transcriptomic data was recently assembled for several species of crustaceans, identification and annotation of the large ABC transporter gene family have been very challenging. In the intertidal copepod Tigriopus japonicus, 46 putative ABC transporters were identified using in silico analysis, and their full-length cDNA sequences were characterized. Phylogenetic analysis revealed that the 46 T. japonicus ABC transporters are classified into eight subfamilies (A-H) that include all the members of all ABC subfamilies, consisting of five ABCA, five ABCB, 17 ABCC, three ABCD, one ABCE, three ABCF, seven ABCG, and five ABCH subfamilies. Of them, unique isotypic expansion of two clades of ABCC1 proteins was observed. Real-time RT-PCR-based heatmap analysis revealed that most T. japonicus ABC genes showed temporal transcriptional expression during copepod development. The overall transcriptional profile demonstrated that half of all T. japonicus ABC genes were strongly associated with at least one developmental stage. Of them, transcripts TJ-ABCH_88708 and TJ-ABCE1 were highly expressed during all developmental stages. The whole set of T. japonicus ABC genes and their phylogenetic relationships will provide a better understanding of the comparative evolution of essential gene family resources in arthropods, including the crustacean copepods.

Evidence from the structure and function of cytochromes c(2) that nonsulfur purple bacterial photosynthesis followed the evolution of oxygen respiration.

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Meyer, Terry; Van Driessche, Gonzalez; Ambler, Richard; Kyndt, John; Devreese, Bart; Van Beeumen, Jozef; Cusanovich, Michael

2010-10-01

Cytochromes c(2) are the nearest bacterial homologs of mitochondrial cytochrome c. The sequences of the known cytochromes c(2) can be placed in two subfamilies based upon insertions and deletions, one subfamily is most like mitochondrial cytochrome c (the small C2s, without significant insertions and deletions), and the other, designated large C2, shares 3- and 8-residue insertions as well as a single-residue deletion. C2s generally function between cytochrome bc(1) and cytochrome oxidase in respiration (ca 80 examples known to date) and between cytochrome bc(1) and the reaction center in nonsulfur purple bacterial photosynthesis (ca 21 examples). However, members of the large C2 subfamily are almost always involved in photosynthesis (12 of 14 examples). In addition, the gene for the large C2 (cycA) is associated with those for the photosynthetic reaction center (pufBALM). We hypothesize that the insertions in the large C2s, which were already functioning in photosynthesis, allowed them to replace the membrane-bound tetraheme cytochrome, PufC, that otherwise mediates between the small C2 or other redox proteins and photosynthetic reaction centers. Based upon our analysis, we propose that the involvement of C2 in nonsulfur purple bacterial photosynthesis was a metabolic feature subsequent to the evolution of oxygen respiration.

NCBI nr-aa BLAST: CBRC-ACAR-01-0651 [SEVENS

Lifescience Database Archive (English)

Full Text Available subfamily A member 1 (Ankyrin-like with transmembrane domains protein 1) (Transformation sensitive protein p120) emb|CAA71610.1| ankyrin-like protein [Homo sapiens] O75762 0.46 27% ...

Surface morphology of some articulated corallines from India

Digital Repository Service at National Institute of Oceanography (India)

Kerkar, V.; Iyer, S.D.

Surface structures of seven species belonging to four genera of subfamily Corallinoidae (Fly: Corallinaceae) were microscopically investigated Two distinct surface morphologies were revealed namely a 'Corallina type' (c-type) with round to irregular...

Genomic and expression analysis of the flax (Linum usitatissimum) family of glycosyl hydrolase 35 genes.

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Hobson, Neil; Deyholos, Michael K

2013-05-23

Several β-galactosidases of the Glycosyl Hydrolase 35 (GH35) family have been characterized, and many of these modify cell wall components, including pectins, xyloglucans, and arabinogalactan proteins. The phloem fibres of flax (Linum usitatissimum) have gelatinous-type cell walls that are rich in crystalline cellulose and depend on β-galactosidase activity for their normal development. In this study, we investigate the transcript expression patterns and inferred evolutionary relationships of the complete set of flax GH35 genes, to better understand the functions of these genes in flax and other species. Using the recently published flax genome assembly, we identified 43 β-galactosidase-like (BGAL) genes, based on the presence of a GH35 domain. Phylogenetic analyses of their protein sequences clustered them into eight sub-families. Sub-family B, whose members in other species were known to be expressed in developing flowers and pollen, was greatly under represented in flax (p-value < 0.01). Sub-family A5, whose sole member from arabidopsis has been described as its primary xyloglucan BGAL, was greatly expanded in flax (p-value < 0.01). A number of flax BGALs were also observed to contain non-consensus GH35 active sites. Expression patterns of the flax BGALs were investigated using qRT-PCR and publicly available microarray data. All predicted flax BGALs showed evidence of expression in at least one tissue. Flax has a large number of BGAL genes, which display a distinct distribution among the BGAL sub-families, in comparison to other closely related species with available whole genome assemblies. Almost every flax BGAL was expressed in fibres, the majority of which expressed predominately in fibres as compared to other tissues, suggesting an important role for the expansion of this gene family in the development of this species as a fibre crop. Variations displayed in the canonical GH35 active site suggest a variety of roles unique to flax, which will require

Seed Carotenoid and Tocochromanol Composition of Wild Fabaceae Species Is Shaped by Phylogeny and Ecological Factors

Science.gov (United States)

Fernández-Marín, Beatriz; Míguez, Fátima; Méndez-Fernández, Leire; Agut, Agustí; Becerril, José M.; García-Plazaola, José I.; Kranner, Ilse; Colville, Louise

2017-01-01

Carotenoids distribution and function in seeds have been very scarcely studied, notwithstanding their pivotal roles in plants that include photosynthesis and phytohormone synthesis, pigmentation, membrane stabilization and antioxidant activity. Their relationship with tocochromanols, whose critical role in maintaining seed viability has already been evidenced, and with chlorophylls, whose retention in mature seed is thought to have negative effects on storability, remain also unexplored. Here, we aimed at elucidating seed carotenoids relationship with tocochromanols and chlorophylls with regard to phylogenetic and ecological traits and at understanding their changes during germination. The composition and distribution of carotenoids were investigated in seeds of a wide range of wild species across the Fabaceae (the second-most economically important family after the Poaceae). Photosynthetic pigments and tocochromanols were analyzed by HPLC in mature dry seeds of 50 species representative of 5 subfamilies within the Fabaceae (including taxa that represent all continents, biomes and life forms within the family) and at key timepoints during seedling establishment in three species representative of distinct clades. Total-carotenoids content positively correlated with tocopherols in the basal subfamilies Detarioideae, Cercidoideae, and Dialioideae, and with chlorophylls in the Papilionoideae. Papilionoideae lacked tocotrienols and had the highest total-carotenoids, chlorophyll and γ-tocopherol contents. Interestingly, lutein epoxide was present in 72% of the species including several herbs from different subfamilies. Overall, species original from temperate biomes presented higher carotenoids and lower tocochromanols levels than those from tropical biomes. Also shrub species showed higher carotenoids content than herbs and trees. During germination, total content of photosynthetic pigments increased in parallel to changes in relative abundance of carotenoids

Discovery of germacrene A synthases in Barnadesia spinosa: The first committed step in sesquiterpene lactone biosynthesis in the basal member of the Asteraceae

International Nuclear Information System (INIS)

Nguyen, Trinh-Don; Faraldos, Juan A.; Vardakou, Maria; Salmon, Melissa; O'Maille, Paul E.; Ro, Dae-Kyun

2016-01-01

The Andes-endemic Barnadesioideae lineage is the oldest surviving and phylogenetically basal subfamily of the Asteraceae (Compositae), a prolific group of flowering plants with world-wide distribution (∼24,000 species) marked by a rich diversity of sesquiterpene lactones (STLs). Intriguingly, there is no evidence that members of the Barnadesioideae produce STLs, specialized metabolites thought to have contributed to the adaptive success of the Asteraceae family outside South America. The biosynthesis of STLs requires the intimate expression and functional integration of germacrene A synthase (GAS) and germacrene A oxidase (GAO) to sequentially cyclize and oxidize farnesyl diphosphate into the advanced intermediate germacrene A acid leading to diverse STLs. Our previous discovery of GAO activity conserved across all major subfamilies of Asteraceae, including the phylogenetically basal lineage of Barnadesioideae, prompted further investigation of the presence of the gateway GAS in Barnadesioideae. Herein we isolated two terpene synthases (BsGAS1/BsGAS2) from the basal Barnadesia spinosa (Barnadesioideae) that displayed robust GAS activity when reconstituted in yeast and characterized in vitro. Despite the apparent lack of STLs in the Barnadesioideae, this work unambiguously confirms the presence of GAS in the basal genera of the Asteraceae. Phylogenetic analysis reveals that the two BsGASs fall into two distinct clades of the Asteraceae's GASs, and BsGAS1 clade is only retained in the evolutionary closer Cichorioideae subfamily, implicating BsGAS2 is likely the ancestral base of most GASs found in the lineages outside the Barnadesioideae. Taken together, these results show the enzymatic capacities of GAS and GAO emerged prior to the subsequent radiation of STL-producing Asteraceae subfamilies. - Highlights: • Sesquiterpene lactones are characteristic metabolites in Asteraceae family. • Barnadesioideae is the basal lineage of all Asteraceae plants

The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization.

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Qian Yan

Full Text Available Basic/helix-loop-helix (bHLH proteins comprise one of the largest transcription factor families and play important roles in diverse cellular and molecular processes. Comprehensive analyses of the composition and evolution of the bHLH family in cotton are essential to elucidate their functions and the molecular basis of cotton development. By searching bHLH homologous genes in sequenced diploid cotton genomes (Gossypium raimondii and G. arboreum, a set of cotton bHLH reference genes containing 289 paralogs were identified and named as GobHLH001-289. Based on their phylogenetic relationships, these cotton bHLH proteins were clustered into 27 subfamilies. Compared to those in Arabidopsis and cacao, cotton bHLH proteins generally increased in number, but unevenly in different subfamilies. To further uncover evolutionary changes of bHLH genes during tetraploidization of cotton, all genes of S5a and S5b subfamilies in upland cotton and its diploid progenitors were cloned and compared, and their transcript profiles were determined in upland cotton. A total of 10 genes of S5a and S5b subfamilies (doubled from A- and D-genome progenitors maintained in tetraploid cottons. The major sequence changes in upland cotton included a 15-bp in-frame deletion in GhbHLH130D and a long terminal repeat retrotransposon inserted in GhbHLH062A, which eliminated GhbHLH062A expression in various tissues. The S5a and S5b bHLH genes of A and D genomes (except GobHLH062 showed similar transcription patterns in various tissues including roots, stems, leaves, petals, ovules, and fibers, while the A- and D-genome genes of GobHLH110 and GobHLH130 displayed clearly different transcript profiles during fiber development. In total, this study represented a genome-wide analysis of cotton bHLH family, and revealed significant changes in sequence and expression of these genes in tetraploid cottons, which paved the way for further functional analyses of bHLH genes in the cotton genus.

A large 28S rDNA-based phylogeny confirms the limitations of established morphological characters for classification of proteocephalidean tapeworms (Platyhelminthes, Cestoda

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Alain de Chambrier

2015-04-01

Full Text Available Proteocephalidean tapeworms form a diverse group of parasites currently known from 315 valid species. Most of the diversity of adult proteocephalideans can be found in freshwater fishes (predominantly catfishes, a large proportion infects reptiles, but only a few infect amphibians, and a single species has been found to parasitize possums. Although they have a cosmopolitan distribution, a large proportion of taxa are exclusively found in South America. We analyzed the largest proteocephalidean cestode molecular dataset to date comprising more than 100 species (30 new, including representatives from 54 genera (80% and all subfamilies, thus significantly improving upon previous works to develop a molecular phylogeny for the group. The Old World origin of proteocephalideans is confirmed, with their more recent expansion in South America. The earliest diverging lineages are composed of Acanthotaeniinae and Gangesiinae but most of the presently recognized subfamilies (and genera appear not to be monophyletic; a deep systematic reorganization of the order is thus needed and the present subfamilial system should be abandoned. The main characters on which the classical systematics of the group has been built, such as scolex morphology or relative position of genital organs in relation to the longitudinal musculature, are of limited value, as demonstrated by the very weak support for morphologically-defined subfamilies. However, new characters, such as the pattern of uterus development, relative ovary size, and egg structure have been identified, which may be useful in defining phylogenetically well-supported subgroups. A strongly supported lineage infecting various snakes from a wide geographical distribution was found. Although several improvements over previous works regarding phylogenetic resolution and taxon coverage were achieved in this study, the major polytomy in our tree, composed largely of siluriform parasites from the Neotropics, remained

A large 28S rDNA-based phylogeny confirms the limitations of established morphological characters for classification of proteocephalidean tapeworms (Platyhelminthes, Cestoda).

Science.gov (United States)

de Chambrier, Alain; Waeschenbach, Andrea; Fisseha, Makda; Scholz, Tomáš; Mariaux, Jean

2015-01-01

Proteocephalidean tapeworms form a diverse group of parasites currently known from 315 valid species. Most of the diversity of adult proteocephalideans can be found in freshwater fishes (predominantly catfishes), a large proportion infects reptiles, but only a few infect amphibians, and a single species has been found to parasitize possums. Although they have a cosmopolitan distribution, a large proportion of taxa are exclusively found in South America. We analyzed the largest proteocephalidean cestode molecular dataset to date comprising more than 100 species (30 new), including representatives from 54 genera (80%) and all subfamilies, thus significantly improving upon previous works to develop a molecular phylogeny for the group. The Old World origin of proteocephalideans is confirmed, with their more recent expansion in South America. The earliest diverging lineages are composed of Acanthotaeniinae and Gangesiinae but most of the presently recognized subfamilies (and genera) appear not to be monophyletic; a deep systematic reorganization of the order is thus needed and the present subfamilial system should be abandoned. The main characters on which the classical systematics of the group has been built, such as scolex morphology or relative position of genital organs in relation to the longitudinal musculature, are of limited value, as demonstrated by the very weak support for morphologically-defined subfamilies. However, new characters, such as the pattern of uterus development, relative ovary size, and egg structure have been identified, which may be useful in defining phylogenetically well-supported subgroups. A strongly supported lineage infecting various snakes from a wide geographical distribution was found. Although several improvements over previous works regarding phylogenetic resolution and taxon coverage were achieved in this study, the major polytomy in our tree, composed largely of siluriform parasites from the Neotropics, remained unresolved and

Structural analysis of alkaline β-mannanase from alkaliphilic Bacillus sp. N16-5: implications for adaptation to alkaline conditions.

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Yueju Zhao

Full Text Available Significant progress has been made in isolating novel alkaline β-mannanases, however, there is a paucity of information concerning the structural basis for alkaline tolerance displayed by these β-mannanases. We report the catalytic domain structure of an industrially important β-mannanase from the alkaliphilic Bacillus sp. N16-5 (BSP165 MAN at a resolution of 1.6 Å. This enzyme, classified into subfamily 8 in glycosyl hydrolase family 5 (GH5, has a pH optimum of enzymatic activity at pH 9.5 and folds into a classic (β/α(8-barrel. In order to gain insight into molecular features for alkaline adaptation, we compared BSP165 MAN with previously reported GH5 β-mannanases. It was revealed that BSP165 MAN and other subfamily 8 β-mannanases have significantly increased hydrophobic and Arg residues content and decreased polar residues, comparing to β-mannanases of subfamily 7 or 10 in GH5 which display optimum activities at lower pH. Further, extensive structural comparisons show alkaline β-mannanases possess a set of distinctive features. Position and length of some helices, strands and loops of the TIM barrel structures are changed, which contributes, to a certain degree, to the distinctly different shaped (β/α(8-barrels, thus affecting the catalytic environment of these enzymes. The number of negatively charged residues is increased on the molecular surface, and fewer polar residues are exposed to the solvent. Two amino acid substitutions in the vicinity of the acid/base catalyst were proposed to be possibly responsible for the variation in pH optimum of these homologous enzymes in subfamily 8 of GH5, identified by sequence homology analysis and pK(a calculations of the active site residues. Mutational analysis has proved that Gln91 and Glu226 are important for BSP165 MAN to function at high pH. These findings are proposed to be possible factors implicated in the alkaline adaptation of GH5 β-mannanases and will help to further

The Interleukin-20 Cytokine Family in Liver Disease

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Esther Caparrós

2018-05-01

Full Text Available The three main causes of inflammation and chronic injury in the liver are viral hepatitis, alcohol consumption, and non-alcoholic steatohepatitis, all of which can lead to liver fibrosis, cirrhosis, and hepatocellular carcinoma, which in turn may prompt the need for liver transplant. The interleukin (IL-20 is a subfamily part of the IL-10 family of cytokines that helps the liver respond to damage and disease, they participate in the control of tissue homeostasis, and in the immunological responses developed in this organ. The best-studied member of the family in inflammatory balance of the liver is the IL-22 cytokine, which on the one hand may have a protective role in fibrosis progression but on the other may induce liver tissue susceptibility in hepatocellular carcinoma development. Other members of the family might also carry out this dual function, as some of them share IL receptor subunits and signal through common intracellular pathways. Investigators are starting to consider the potential for targeting IL-20 subfamily members in liver disease. The recently explored role of miRNA in the transcriptional regulation of IL-22 and IL-24 opens the door to promising new approaches for controlling the local immune response and limiting organ injury. The IL-20RA cytokine receptor has also been classified as being under miRNA control in non-alcoholic steatohepatitis. Moreover, researchers have proposed combining anti-inflammatory drugs with IL-22 as a hepatoprotective IL for alcoholic liver disease (ALD treatment, and clinical trials of ILs for managing severe alcoholic-derived liver degeneration are ongoing. In this review, we focus on exploring the role of the IL-20 subfamily of cytokines in viral hepatitis, ALD, non-alcoholic steatohepatitis, and hepatocellular carcinoma, as well as delineating the main strategies explored so far in terms of therapeutic possibilities of the IL-20 subfamily of cytokines in liver disease.

Evolutionary history of callose synthases in terrestrial plants with emphasis on proteins involved in male gametophyte development.

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Lenka Záveská Drábková

Full Text Available Callose is a plant-specific polysaccharide (β-1,3-glucan playing an important role in angiosperms in many developmental processes and responses to biotic and abiotic stresses. Callose is synthesised at the plasma membrane of plant cells by callose synthase (CalS and, among others, represents the main polysaccharide in the callose wall surrounding the tetrads of developing microspores and in the growing pollen tube wall. CalS proteins involvement in spore development is a plesiomorphic feature of terrestrial plants, but very little is known about their evolutionary origin and relationships amongst the members of this protein family. We performed thorough comparative analyses of callose synthase family proteins from major plant lineages to determine their evolutionary history across the plant kingdom. A total of 1211 candidate CalS sequences were identified and compared amongst diverse taxonomic groups of plants, from bryophytes to angiosperms. Phylogenetic analyses identified six main clades of CalS proteins and suggested duplications during the evolution of specialised functions. Twelve family members had previously been identified in Arabidopsis thaliana. We focused on five CalS subfamilies directly linked to pollen function and found that proteins expressed in pollen evolved twice. CalS9/10 and CalS11/12 formed well-defined clades, whereas pollen-specific CalS5 was found within subfamilies that mostly did not express in mature pollen vegetative cell, although were found in sperm cells. Expression of five out of seven mature pollen-expressed CalS genes was affected by mutations in bzip transcription factors. Only three subfamilies, CalS5, CalS10, and CalS11, however, formed monophyletic, mostly conserved clades. The pairs CalS9/CalS10, CalS11/CalS12 and CalS3 may have diverged after angiosperms diversified from lycophytes and bryophytes. Our analysis of fully sequenced plant proteins identified new evolutionary lineages of callose synthase

Genome-wide analysis of putative peroxiredoxin in unicellular and filamentous cyanobacteria

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Cui Hongli

2012-11-01

Full Text Available Abstract Background Cyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats. Peroxiredoxin (PRX is an important protein that plays essential roles in protecting own cells against reactive oxygen species (ROS. PRXs have been identified from mammals, fungi and higher plants. However, knowledge on cyanobacterial PRXs still remains obscure. With the availability of 37 sequenced cyanobacterial genomes, we performed a comprehensive comparative analysis of PRXs and explored their diversity, distribution, domain structure and evolution. Results Overall 244 putative prx genes were identified, which were abundant in filamentous diazotrophic cyanobacteria, Acaryochloris marina MBIC 11017, and unicellular cyanobacteria inhabiting freshwater and hot-springs, while poor in all Prochlorococcus and marine Synechococcus strains. Among these putative genes, 25 open reading frames (ORFs encoding hypothetical proteins were identified as prx gene family members and the others were already annotated as prx genes. All 244 putative PRXs were classified into five major subfamilies (1-Cys, 2-Cys, BCP, PRX5_like, and PRX-like according to their domain structures. The catalytic motifs of the cyanobacterial PRXs were similar to those of eukaryotic PRXs and highly conserved in all but the PRX-like subfamily. Classical motif (CXXC of thioredoxin was detected in protein sequences from the PRX-like subfamily. Phylogenetic tree constructed of catalytic domains coincided well with the domain structures of PRXs and the phylogenies based on 16s rRNA. Conclusions The distribution of genes encoding PRXs in different unicellular and filamentous cyanobacteria especially those sub-families like PRX-like or 1-Cys PRX correlate with the genome size, eco-physiology, and physiological properties of the organisms. Cyanobacterial and eukaryotic PRXs share similar conserved motifs, indicating that cyanobacteria adopt similar catalytic

Genome-wide analysis of putative peroxiredoxin in unicellular and filamentous cyanobacteria.

Science.gov (United States)

Cui, Hongli; Wang, Yipeng; Wang, Yinchu; Qin, Song

2012-11-16

Cyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats. Peroxiredoxin (PRX) is an important protein that plays essential roles in protecting own cells against reactive oxygen species (ROS). PRXs have been identified from mammals, fungi and higher plants. However, knowledge on cyanobacterial PRXs still remains obscure. With the availability of 37 sequenced cyanobacterial genomes, we performed a comprehensive comparative analysis of PRXs and explored their diversity, distribution, domain structure and evolution. Overall 244 putative prx genes were identified, which were abundant in filamentous diazotrophic cyanobacteria, Acaryochloris marina MBIC 11017, and unicellular cyanobacteria inhabiting freshwater and hot-springs, while poor in all Prochlorococcus and marine Synechococcus strains. Among these putative genes, 25 open reading frames (ORFs) encoding hypothetical proteins were identified as prx gene family members and the others were already annotated as prx genes. All 244 putative PRXs were classified into five major subfamilies (1-Cys, 2-Cys, BCP, PRX5_like, and PRX-like) according to their domain structures. The catalytic motifs of the cyanobacterial PRXs were similar to those of eukaryotic PRXs and highly conserved in all but the PRX-like subfamily. Classical motif (CXXC) of thioredoxin was detected in protein sequences from the PRX-like subfamily. Phylogenetic tree constructed of catalytic domains coincided well with the domain structures of PRXs and the phylogenies based on 16s rRNA. The distribution of genes encoding PRXs in different unicellular and filamentous cyanobacteria especially those sub-families like PRX-like or 1-Cys PRX correlate with the genome size, eco-physiology, and physiological properties of the organisms. Cyanobacterial and eukaryotic PRXs share similar conserved motifs, indicating that cyanobacteria adopt similar catalytic mechanisms as eukaryotes. All cyanobacterial PRX proteins

A plastid phylogeny and character evolution of the Old World fern genus Pyrrosia (Polypodiaceae) with the description of a new genus: Hovenkampia (Polypodiaceae).

Science.gov (United States)

Zhou, Xin-Mao; Zhang, Liang; Chen, Cheng-Wei; Li, Chun-Xiang; Huang, Yao-Moan; Chen, De-Kui; Lu, Ngan Thi; Cicuzza, Daniele; Knapp, Ralf; Luong, Thien Tam; Nitta, Joel H; Gao, Xin-Fen; Zhang, Li-Bing

2017-09-01

The Old World fern genus Pyrrosia (Polypodiaceae) offers a rare system in ferns to study morphological evolution because almost all species of this genus are well studied for their morphology, anatomy, and spore features, and various hypotheses have been proposed in terms of the phylogeny and evolution in this genus. However, the molecular phylogeny of the genus lags behind. The monophyly of the genus has been uncertain and a modern phylogenetic study of the genus based on molecular data has been lacking. In the present study, DNA sequences of five plastid markers of 220 accessions of Polypodiaceae representing two species of Drymoglossum, 14 species of Platycerium, 50 species of Pyrrosia, and the only species of Saxiglossum (subfamily Platycerioideae), and 12 species of other Polypodiaceae representing the remaining four subfamilies are used to infer a phylogeny of the genus. Major results and conclusions of this study include: (1) Pyrrosia as currently circumscribed is paraphyletic in relation to Platycerium and can be divided into two genera: Pyrrosia s.s. and Hovenkampia (gen. nov.), with Hovenkampia and Platycerium forming a strongly supported clade sister to Pyrrosia s.s.; (2) Subfamily Platycerioideae should contain three genera only, Hovenkampia, Platycerium, and Pyrrosia s.s.; (3) Based on the molecular phylogeny, macromorphology, anatomical features, and spore morphology, four major clades in the genus are identified and three of the four are further resolved into four, four, and six subclades, respectively; (4) Three species, P. angustissima, P. foveolata, and P. mannii, not assigned to any groups by Hovenkamp (1986) because of their unusual morphology, each form monospecific clades; (5) Drymoglossum is not monophyletic and those species previously assigned to this genus are resolved in two different subclades; (6) Saxiglossum is resolved as the first lineage in the Niphopsis clade; and (7) The evolution of ten major morphological characters in the

Phylogenetic Analysis, Lineage-Specific Expansion and Functional Divergence of seed dormancy 4-Like Genes in Plants.

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Saminathan Subburaj

Full Text Available The rice gene seed dormancy 4 (OsSdr4 functions in seed dormancy and is a major factor associated with pre-harvest sprouting (PHS. Although previous studies of this protein family were reported for rice and other species, knowledge of the evolution of genes homologous to OsSdr4 in plants remains inadequate. Fifty four Sdr4-like (hereafter designated Sdr4L genes were identified in nine plant lineages including 36 species. Phylogenetic analysis placed these genes in eight subfamilies (I-VIII. Genes from the same lineage clustered together, supported by analysis of conserved motifs and exon-intron patterns. Segmental duplications were present in both dicot and monocot clusters, while tandemly duplicated genes occurred only in monocot clusters indicating that both tandem and segmental duplications contributed to expansion of the grass I and II subfamilies. Estimation of the approximate ages of the duplication events indicated that ancestral Sdr4 genes evolved from a common angiosperm ancestor, about 160 million years ago (MYA. Moreover, diversification of Sdr4L genes in mono and dicot plants was mainly associated with genome-wide duplication and speciation events. Functional divergence was observed in all subfamily pairs, except IV/VIIIa. Further analysis indicated that functional constraints between subfamily pairs I/II, I/VIIIb, II/VI, II/VIIIb, II/IV, and VI/VIIIb were statistically significant. Site and branch-site model analyses of positive selection suggested that these genes were under strong adaptive selection pressure. Critical amino acids detected for both functional divergence and positive selection were mostly located in the loops, pointing to functional importance of these regions in this protein family. In addition, differential expression studies by transcriptome atlas of 11 Sdr4L genes showed that the duplicated genes may have undergone divergence in expression between plant species. Our findings showed that Sdr4L genes are

Floral vasculature and trichomes of common Indian Scrophulariaceae

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P. C. Datta

2015-01-01

Full Text Available The floral anatomy of 24 species of Scrophulariaceae was studied. The results show that although, clear anatomical bases to differentiate taxa are absent, the Pennell classification of subfamilies is strongly supported.

Malesian and Australian Tournefortia transferred to Heliotropium and notes on delimitation of Boraginaceae

NARCIS (Netherlands)

Craven, L.A.

2005-01-01

Boraginaceae is expanded to comprise seven subfamilies, two of which are based on Hydrophyllaceae and Lennoaceae, respectively. The type species of Tournefortia sect. Tournefortia is transferred to Heliotropium, as are its Malesian–Australian representatives.

responsive transcription factor from Hevea brasiliensis Muell. Arg.

African Journals Online (AJOL)

Jane

2011-08-29

Aug 29, 2011 ... members of CBF/DREB subfamily from different plant species. Quantitative ..... mechanisms of hormonal (ethylene) stimulation. In: D'Auzac J, .... wide interacting effects of sucrose and herbicide-mediated stress in. Arabidopsis ...

Antennal sensilla of grasshoppers (Orthoptera: Acrididae) in relation ...

Indian Academy of Sciences (India)

Unknown

number of antennal sensillae varied among different sexes, subfamilies, ... Males showed significantly more sensillae than females, due to presence of more short basiconic and ..... were conducted to the primary olfactory center of the brain,.

Transposon display supports transpositional activity of P elements in ...

Indian Academy of Sciences (India)

. Abstract. Mobilization of two P element subfamilies (canonical and O-type) from Drosophila sturtevanti and D. saltans was evaluated for copy number and transposition activity using the transposon display (TD) technique. Pairwise distances ...

A burst of ABC genes in the genome of the polyphagous spider mite Tetranychus urticae.

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Dermauw, Wannes; Osborne, Edward John; Clark, Richard M; Grbić, Miodrag; Tirry, Luc; Van Leeuwen, Thomas

2013-05-10

The ABC (ATP-binding cassette) gene superfamily is widespread across all living species. The majority of ABC genes encode ABC transporters, which are membrane-spanning proteins capable of transferring substrates across biological membranes by hydrolyzing ATP. Although ABC transporters have often been associated with resistance to drugs and toxic compounds, within the Arthropoda ABC gene families have only been characterized in detail in several insects and a crustacean. In this study, we report a genome-wide survey and expression analysis of the ABC gene superfamily in the spider mite, Tetranychus urticae, a chelicerate ~ 450 million years diverged from other Arthropod lineages. T. urticae is a major agricultural pest, and is among of the most polyphagous arthropod herbivores known. The species resists a staggering array of toxic plant secondary metabolites, and has developed resistance to all major classes of pesticides in use for its control. We identified 103 ABC genes in the T. urticae genome, the highest number discovered in a metazoan species to date. Within the T. urticae ABC gene set, all members of the eight currently described subfamilies (A to H) were detected. A phylogenetic analysis revealed that the high number of ABC genes in T. urticae is due primarily to lineage-specific expansions of ABC genes within the ABCC, ABCG and ABCH subfamilies. In particular, the ABCC subfamily harbors the highest number of T. urticae ABC genes (39). In a comparative genomic analysis, we found clear orthologous relationships between a subset of T. urticae ABC proteins and ABC proteins in both vertebrates and invertebrates known to be involved in fundamental cellular processes. These included members of the ABCB-half transporters, and the ABCD, ABCE and ABCF families. Furthermore, one-to-one orthologues could be distinguished between T. urticae proteins and human ABCC10, ABCG5 and ABCG8, the Drosophila melanogaster sulfonylurea receptor and ecdysone-regulated transporter E

Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics

DEFF Research Database (Denmark)

Sicheritz-Pontén, Thomas; Noel, CJ; Diaz, N

2010-01-01

Trichomonas vaginalis is the most common non-viral human sexually transmitted pathogen and importantly, contributes to facilitating the spread of HIV. Yet very little is known about its surface and secreted proteins mediating interactions with, and permitting the invasion and colonisation of...... potential extracellular proteins for the pathogen. A broad range of microorganisms encoding BspA-like proteins was identified and these are mainly known to live on mucosal surfaces, among these T. vaginalis is endowed with the largest gene family. Over 180 TvBspA proteins with inferred transmembrane domains...... were characterized by a considerable structural diversity between their TpLRR and other types of repetitive sequences and two subfamilies possessed distinct classic sorting signal motifs for endocytosis. One TvBspA subfamily also shared a glycine-rich protein domain with proteins from Clostridium...

Early Bashkirian Rugosa (Anthozoa) from the Donets Basin (Ukraine). Part 6. The Family Aulophyllidae Dybowski, 1873

Science.gov (United States)

Fedorowski, Jerzy

2017-12-01

Seven genera (one new), belonging to four subfamilies, seven named species (six new), four species left in open nomenclature and two specimens included in this paper as unnamed Aulophyllidae are described from strata ranging from the lowermost Bashkirian Limestone D510 to the lower Bashkirian Limestone F1. A new genus: Voragoaxum and six new species: Dibunophyllum medium, Dibunophylloides columnatus, D. paulus, D. similis, Voragoaxum cavum and Rozkowskia lenta are introduced. Comparison of the ontogeny of the earliest Bashkirian species of Nina Fedorowski, 2017a and Dibunophylloides Fomichev, 1953 suggest the derivation by descent of the Family Bothrophyllidae from the Subfamily Dibunophyllinae. This means that true bothrophylla are absent in the Mississippian strata of the Western European Province and, perhaps, in the contemporaneous strata of other areas as well.

A Preliminary Survey of Species Composition of Termites (Insecta: Isoptera) in Samunsam Wildlife Sanctuary, Sarawak.

Science.gov (United States)

Jamil, Norsyarizan; Ismail, Wan Nurainie Wan; Abidin, Siti Shamimi; Amaran, Mazdan Ali; Hazali, Ratnawati

2017-07-01

A survey on termite species composition was conducted in Samunsam Wildlife Sanctuary, Sarawak in February 2015. Overall 19 species of termite belonging to 13 genera and 8 subfamilies was found in the sanctuary. It was recorded the subfamily of Termitinae had the highest number of species (6 species, equal to 31.58% of total species), followed by Nasutermitinae (3 species, 15.79%), Macrotermitinae, Amitermitinae, Rhinotermitinae, Coptotermitinae, (2 species, 10.53% respectively), and Heterotermitinae, Termitogetoninae (1 species, 5.26% respectively). Since this rapid survey is the first termite assemblage representation in Samunsam Wildlife Sanctuary, the preliminary result may serve as the baseline data for termite composition in the area. Therefore, a whole coverage for the area within this sanctuary would definitely increase the number of termite species found in the sanctuary.

Towards an integrated understanding of the consequences of fungus domestication on the fungus-growing termite gut microbiota

DEFF Research Database (Denmark)

Thomas-Poulsen, Michael

2015-01-01

Approximately 30 million years ago (MYA), the subfamily of higher termites Macrotermitinae domesticated a fungus, Termitomyces, as the main plant decomposer and food source for the termite host. The origin of fungiculture shifted the composition of the termite gut microbiota, and some of the func......Approximately 30 million years ago (MYA), the subfamily of higher termites Macrotermitinae domesticated a fungus, Termitomyces, as the main plant decomposer and food source for the termite host. The origin of fungiculture shifted the composition of the termite gut microbiota, and some...... will be powerful, particularly if executed in comparative analyses across the well-established congruent termite-fungus phylogenies. This will allow for testing if gut communities have evolved in parallel with their hosts, with implications for our general understanding of the evolution of gut symbiont communities...

A new genus and species of micro bee fly from the Earliest Eocene French amber (Diptera: Mythicomyiidae: Psiloderoidinae).

Science.gov (United States)

Myskowiak, Justine; Garrouste, Romain; Nel, Andre

2016-05-26

Mythicomyiidae, or micro bee flies, are tiny flies (0.5-5.0 mm) that are found throughout most parts of the world except the highest altitudes and latitudes (Greathead & Evenhuis 2001). Including all extinct and extant taxa, the Mythicomyiidae currently comprise more than 380 valid taxonomic species distributed among 30 genera. The subfamily Psiloderoidinae is especially well represented among the fossil Mythicomyiidae by seven Cretaceous or Cenozoic genera. We here describe a new genus and a new species of this subfamily based on fossils from the Earliest Eocene of Oise (France). A Psiloderoidinae, Proplatypygus matilei Nel & DePloëg, 2004, is already described in this amber. Another mythicomyiid, Eurodoliopteryx inexpectatus Nel, 2006, is the most frequent bombylioid in this amber (Nel & DePloëg, 2004; Nel, 2006).

Reconstruction of mitogenomes by NGS and phylogenetic implications for leaf beetles.

Science.gov (United States)

Song, Nan; Yin, Xinming; Zhao, Xincheng; Chen, Junhua; Yin, Jian

2017-11-30

Mitochondrial genome (mitogenome) sequences are frequently used to infer phylogenetic relationships of insects at different taxonomic levels. Next-generation sequencing (NGS) techniques are revolutionizing many fields of biology, and allow for acquisition of insect mitogenomes for large number of species simultaneously. In this study, 20 full or partial mitogenomes were sequenced from pooled genomic DNA samples by NGS for leaf beetles (Chrysomelidae). Combined with published mitogenome sequences, a higher level phylogeny of Chrysomelidae was reconstructed under maximum likelihood and Bayesian inference with different models and various data treatments. The results revealed support for a basal position of Bruchinae within Chrysomelidae. In addition, two major subfamily groupings were recovered: one including seven subfamilies, namely Donaciinae, Criocerinae, Spilopyrinae, Cassidinae, Cryptocephalinae, Chlamisinae and Eumolpinae, another containing a non-monophyletic Chrysomelinae and a monophyletic Galerucinae.

Seed morphology and its taxonomic significance in the family malvaceae

International Nuclear Information System (INIS)

Abid, R.; Ather, A.

2016-01-01

The seed morphological studies of 75 taxa belonging to 6 sub-families of the family Malvaceae were carried out from Pakistan. In Pakistan the family Malvaceae is represented by 6 sub-families viz., Byttnerioideae, Dombeyoideae, Malvoideae, Bombacoideae, Helicteroideae and Sterculioideae. The seed macro and micro morphological characters are examined, using light (LM) and scanning electron microscopy (SEM). Detailed seed morphological descriptions, micrographs and keys based on seed characters are also provided. A variety in various quantitative and qualitative seed characters was observed. The micro-morphological characters of seeds are quite significant to strengthen the taxonomic decisions within the family Malvaceae at various levels. The data obtained from the seed morphological characters were analyzed numerically to trace out the phylogenetic affinities for the taxa within the family Malvaceae from Pakistan. (author)

molecular mechanisms of metabolic rate depression in animals

African Journals Online (AJOL)

adjustments and the role of stress-induced gene expression in producing specific adaptive proteins. Protein ..... Furthermore, rat and bat brain PKC differed strongly in their responses to ...... The stress-activated protein kinase subfamily ofc-jun.

GenBank blastx search result: AK241408 [KOME

Lifescience Database Archive (English)

Full Text Available dependent regulator of chromatin (subfamily a, member 1), the 5' end of the OCRL gene for oculocerebrorenal syndrome of Lowe and two CpG islands, complete sequence. PRI 1e-21 1 ...

GenBank blastx search result: AK242828 [KOME

Lifescience Database Archive (English)

Full Text Available dependent regulator of chromatin (subfamily a, member 1), the 5' end of the OCRL gene for oculocerebrorenal syndrome of Lowe and two CpG islands, complete sequence. PRI 3e-51 1 ...

ANTELOPES IN THE PLEISTOCENE OF SOUTHERN AFRICA This ...

African Journals Online (AJOL)

respectively in the National Museum, Bloemfontein, and the South African Museum, Cape. Town. Four faunal ... as tribes rather than subfamilies. .... recorded during this stage only in the central and northern Transvaal and in northern Zululand.

Description of the immature stages and life history of Euselasia (Lepidoptera: Riodinidae) on Miconia (Melastomataceae) in Costa Rica

Science.gov (United States)

K. Nishida

2010-01-01

The immature stages and life histories of Euselasia chrysippe (Bates, 1866) and E. bettina (Hewitson, 1869) are described, providing the first detailed morphological characters for the subfamily Euselasiinae. The larvae of Euselasia chrysippe and E. bettina ...

A re-evaluation of the phylogeny of Old World Treefrogs | Channing ...

African Journals Online (AJOL)

Seven subfamilies are recognized; six are monophyletic (Hyperoliidae: Hyperoliinae, Kassininae, Leptopelinae, Tachycneminae; Rhacophoridae: Buergeriinae, Mantellinae), while the Rhacophorinae are polyphyletic. The taxonomic changes from the standard Amphibian Species of the World (Frost 1985) proposed are: ...

MOLECULAR PHYLOGENY OF LARGE MILIOLID FORAMINIFERA. (R825869)

Science.gov (United States)

AbstractThe foraminiferal superfamily Soritacea belongs to the suborder Miliolina and is divided in two families, Peneroplidae and Soritidae, the latter one comprising two subfamilies, Archaiasinae and Soritinae. Phylogenetic relationships of 11 genera of soritid fora...

New faunistic data on the family Braconidae (Hymenoptera from Korea

Directory of Open Access Journals (Sweden)

Tae-Ho An

2014-12-01

Full Text Available Twenty-one species of the four genera in the family Braconidae (Hymenoptera are reported for the first time in Korea. These species belong to the subfamily Euphorinae (Braconidae. Faunistic and distribution data are included.

A molecular analysis of the Gelechiidae (Lepidoptera, Gelechioidea) with an interpretative grouping of its taxa

DEFF Research Database (Denmark)

Karsholt, Ole; Mutanen, Marko; Lee, Sangmi

2013-01-01

, Isocitrate dehydrogenase, Cytosolic malate dehydrogenase, Glyceraldehyde-3-phosphate dehydrogenase and Carbamoylphosphate synthase domain protein). Fifty-two taxa representing nearly all established subfamilies and tribes of Gelechiidae, and about 10% of described gelechiid genera, in addition to five...

Feline immunodeficiency virus: Studies on pathogenesis and vaccine development

NARCIS (Netherlands)

C.H.J. Siebelink (Kees)

1995-01-01

textabstractFeline immunodeficiency virus (FIV) is classified as a member of the genus Lentivirus (subfamily Lentivirinae) of the Retroviridae family on basis of its morphology, biochemical characteristics, genomic organization, Mg'+ dependent reverse transcriptase, and nucleotide sequence homology

Biotransformation of Я-estradiol isolated from Sonchus eruca

African Journals Online (AJOL)

Administrator

2011-06-20

Jun 20, 2011 ... Sonchus eruca belonging to the family of asteraceae. The asteraceae or ... 23000 species, distributed in three sub-families and 17 tribes. It is also ..... lipoglycopeptide antibiotic A40926 with immobilized cells of. Actinoplanes ...

Arabidopsis CDS blastp result: AK241043 [KOME

Lifescience Database Archive (English)

Full Text Available upted by a stop codon, creating non-consensus donor and acceptor splice sites. 2e-41 ... ...tical to SP|P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interr

Arabidopsis CDS blastp result: AK243135 [KOME

Lifescience Database Archive (English)

Full Text Available upted by a stop codon, creating non-consensus donor and acceptor splice sites. 7e-43 ... ...tical to SP|P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interr

Molecular phylogeny and divergence times of Malagasy tenrecs: influence of data partitioning and taxon sampling on dating analyses

NARCIS (Netherlands)

Poux, C.; Madsen, O.; Glos, J.; Jong, de W.W.; Vences, M.

2008-01-01

Background Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec, Echinops, Setifer and Hemicentetes; Oryzorictinae: Oryzorictes, Limnogale and Microgale; Geogalinae:Geogale). The diversity of their morphology

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown

Directory of Open Access Journals (Sweden)

Stanke Mario

2011-04-01

Full Text Available Abstract Background Methods of determining whether or not any particular HIV-1 sequence stems - completely or in part - from some unknown HIV-1 subtype are important for the design of vaccines and molecular detection systems, as well as for epidemiological monitoring. Nevertheless, a single algorithm only, the Branching Index (BI, has been developed for this task so far. Moving along the genome of a query sequence in a sliding window, the BI computes a ratio quantifying how closely the query sequence clusters with a subtype clade. In its current version, however, the BI does not provide predicted boundaries of unknown fragments. Results We have developed Unknown Subtype Finder (USF, an algorithm based on a probabilistic model, which automatically determines which parts of an input sequence originate from a subtype yet unknown. The underlying model is based on a simple profile hidden Markov model (pHMM for each known subtype and an additional pHMM for an unknown subtype. The emission probabilities of the latter are estimated using the emission frequencies of the known subtypes by means of a (position-wise probabilistic model for the emergence of new subtypes. We have applied USF to SIV and HIV-1 sequences formerly classified as having emerged from an unknown subtype. Moreover, we have evaluated its performance on artificial HIV-1 recombinants and non-recombinant HIV-1 sequences. The results have been compared with the corresponding results of the BI. Conclusions Our results demonstrate that USF is suitable for detecting segments in HIV-1 sequences stemming from yet unknown subtypes. Comparing USF with the BI shows that our algorithm performs as good as the BI or better.

Two new species in the subfamily Perlinae (Plecoptera, Perlidae) from China.

Science.gov (United States)

Wang, Hong-Liang; Wang, Guo-Quan; Li, Wei-Hai

2013-01-01

Two species in the genera Neoperla and Kamimuria (Plecoptera: Perlidae) from China are described as new: Kamimuria guangxia sp. n., and Neoperla mesostyla sp. n. The new species are compared to similar taxa.

Genome size variation in Orchidaceae subfamily Apostasioideae: filling the phylogenetic gap

Czech Academy of Sciences Publication Activity Database

Jersáková, Jana; Trávníček, Pavel; Kubátová, B.; Krejčíková, Jana; Urfus, Tomáš; Liu, Z.-J.; Lamb, A.; Ponert, J.; Schulte, K.; Čurn, V.; Vrána, Jan; Leitch, I. J.; Suda, Jan

2013-01-01

Roč. 172, č. 1 (2013), s. 95-105 ISSN 0024-4074 R&D Projects: GA ČR GAP506/12/1320 Institutional support: RVO:67179843 ; RVO:67985939 ; RVO:61389030 Keywords : DNA base content * flow cytometry * nuclear C-value * phylogeny * orchids Subject RIV: EH - Ecology, Behaviour; EF - Botanics (BU-J); EF - Botanics (UEB-Q) Impact factor: 2.699, year: 2013

PANTHER: A Library of Protein Families and Subfamilies Indexed by Function

OpenAIRE

Thomas, Paul D.; Campbell, Michael J.; Kejariwal, Anish; Mi, Huaiyu; Karlak, Brian; Daverman, Robin; Diemer, Karen; Muruganujan, Anushya; Narechania, Apurva

2003-01-01

In the genomic era, one of the fundamental goals is to characterize the function of proteins on a large scale. We describe a method, PANTHER, for relating protein sequence relationships to function relationships in a robust and accurate way. PANTHER is composed of two main components: the PANTHER library (PANTHER/LIB) and the PANTHER index (PANTHER/X). PANTHER/LIB is a collection of “books,” each representing a protein family as a multiple sequence alignment, a Hidden Markov Model (HMM)...

Divergence and adaptive evolution of the gibberellin oxidase genes in plants.

Science.gov (United States)

Huang, Yuan; Wang, Xi; Ge, Song; Rao, Guang-Yuan

2015-09-29

The important phytohormone gibberellins (GAs) play key roles in various developmental processes. GA oxidases (GAoxs) are critical enzymes in GA synthesis pathway, but their classification, evolutionary history and the forces driving the evolution of plant GAox genes remain poorly understood. This study provides the first large-scale evolutionary analysis of GAox genes in plants by using an extensive whole-genome dataset of 41 species, representing green algae, bryophytes, pteridophyte, and seed plants. We defined eight subfamilies under the GAox family, namely C19-GA2ox, C20-GA2ox, GA20ox,GA3ox, GAox-A, GAox-B, GAox-C and GAox-D. Of these, subfamilies GAox-A, GAox-B, GAox-C and GAox-D are described for the first time. On the basis of phylogenetic analyses and characteristic motifs of GAox genes, we demonstrated a rapid expansion and functional divergence of the GAox genes during the diversification of land plants. We also detected the subfamily-specific motifs and potential sites of some GAox genes, which might have evolved under positive selection. GAox genes originated very early-before the divergence of bryophytes and the vascular plants and the diversification of GAox genes is associated with the functional divergence and could be driven by positive selection. Our study not only provides information on the classification of GAox genes, but also facilitates the further functional characterization and analysis of GA oxidases.

Alu repeats as markers for forensic DNA analyses

Energy Technology Data Exchange (ETDEWEB)

Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Kass, D.H. [Louisiana State Univ., New Orleans, LA (United States)] [and others

1994-01-01

The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 98.9% nucleotide identity with the HS subfamily consensus sequence, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 inch and 3 inch unique flanking DNA sequences from each HS Alu that allow the locus to be assayed for the presence or absence of the Alu repeat. The dimorphic HS Alu sequences probably inserted in the human genome after the radiation of modem humans (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project. HS Alu family member insertions differ from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) in that polymorphisms due to Alu insertions arise as a result of a unique event which has occurred only one time in the human population and spread through the population from that point. Therefore, individuals that share HS Alu repeats inherited these elements from a common ancestor. Most VNTR and RFLP polymorphisms may arise multiple times in parallel within a population.

Antioxidant properties and principal phenolic phytochemicals of Indian medicinal plants from Asclepiadoideae and Periplocoideae.

Science.gov (United States)

Surveswaran, Siddharthan; Cai, Yi-Zhong; Xing, Jie; Corke, Harold; Sun, Mei

2010-02-01

The subfamily Asclepiadoideae (Apocynaceae) and the closely-related Periplocoideae are sources of many indigenous Indian medicinal plants. We surveyed antioxidant properties and total phenolic and flavonoid contents of 15 samples, representing 12 Indian medicinal plant species from these subfamilies. Total antioxidant assay was performed using the 2,2-azinobis-3-ethylbenzothiazoline-6-sulfonic acid and ferric-reducing antioxidant power methods. Total phenolic and flavonoid contents were measured using colourimetric methods. Principal phenolic compounds were detected by liquid chromatography-mass spectrometry (LC-MS). The highest antioxidant capacity and high levels of total phenolics and flavonoids were found in the leaves of Decalepis hamiltonii. The stems of Sarcostemma brevistigma exhibited the highest xanthine oxidase (XO) inhibitory activity. The roots of Hemidesmus indicus showed the highest OH(-) radical scavenging activity. In general, Periplocoideae members exhibited higher antioxidant activity than Asclepiadoideae members. The highly significant and positive correlations (R > 0.914) between total antioxidant capacity parameters and total phenolic content indicated that the phenolic compounds contributed significantly to the antioxidant activity of the tested plant samples. The principal phenolic phytochemicals from these plants were identified by LC-MS, including flavonoids, phenolic acids and phenolic terpenoids. Chlorogenic acid and rutin were detected in almost all of the plant samples. The LC-MS analysis provided full fingerprints of the principal phenolic compounds in the medicinal plants from these two subfamilies, which are useful for their authentication and quality evaluation.

Revision of Corallinaceae (Corallinales, Rhodophyta): recognizing Dawsoniolithon gen. nov., Parvicellularium gen. nov. and Chamberlainoideae subfam. nov. containing Chamberlainium gen. nov. and Pneophyllum.

Science.gov (United States)

Caragnano, Annalisa; Foetisch, Alexandra; Maneveldt, Gavin W; Millet, Laurent; Liu, Li-Chia; Lin, Showe-Mei; Rodondi, Graziella; Payri, Claude E

2018-03-25

A multi-gene (SSU, LSU, psbA and COI) molecular phylogeny of the family Corallinaceae (excluding the subfamilies Lithophylloideae and Corallinoideae) showed a paraphyletic grouping of six monophyletic clades. Pneophyllum and Spongites were reassessed and recircumscribed using DNA sequence data integrated with morpho-anatomical comparisons of type material and recently collected specimens. We propose Chamberlainoideae subfam. nov., including the type genus Chamberlainium gen. nov., with C. tumidum comb. nov. as the generitype, and Pneophyllum. Chamberlainium is established to include several taxa previously ascribed to Spongites, the generitype of which currently resides in Neogoniolithoideae. Additionally we propose two new genera, Dawsoniolithon gen. nov. (Metagoniolithoideae), with D. conicum comb. nov. as the generitype and Parvicellularium gen. nov. (subfamily incertae sedis), with P. leonardi sp. nov. as the generitype. Chamberlainoideae has no diagnostic morpho-anatomical features that enable one to assign specimens to it without DNA sequence data, and it is the first subfamily to possess both Type 1 (Chamberlainium) and Type 2 (Pneophyllum) tetra/bisporangial conceptacle roof development. Two characters distinguish Chamberlainium from Spongites: tetra/biasporangial conceptacle chamber diameter (300 μm in Spongites) and tetra/bisporangial conceptacle roof thickness (8 cells in Spongites). Two characters also distinguish Pneophyllum from Dawsoniolithon: tetra/bisporangial conceptacle roof thickness (8 cells in Dawsoniolithon) and thallus construction (dimerous in Pneophyllum vs. monomerous in Dawsoniolithon). This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Transcriptomic insights on the ABC transporter gene family in the salmon louse Caligus rogercresseyi.

Science.gov (United States)

Valenzuela-Muñoz, Valentina; Sturm, Armin; Gallardo-Escárate, Cristian

2015-04-09

ATP-binding cassette (ABC) protein family encode for membrane proteins involved in the transport of various biomolecules through the cellular membrane. These proteins have been identified in all taxa and present important physiological functions, including the process of insecticide detoxification in arthropods. For that reason the ectoparasite Caligus rogercresseyi represents a model species for understanding the molecular underpinnings involved in insecticide drug resistance. llumina sequencing was performed using sea lice exposed to 2 and 3 ppb of deltamethrin and azamethiphos. Contigs obtained from de novo assembly were annotated by Blastx. RNA-Seq analysis was performed and validated by qPCR analysis. From the transcriptome database of C. rogercresseyi, 57 putative members of ABC protein sequences were identified and phylogenetically classified into the eight subfamilies described for ABC transporters in arthropods. Transcriptomic profiles for ABC proteins subfamilies were evaluated throughout C. rogercresseyi development. Moreover, RNA-Seq analysis was performed for adult male and female salmon lice exposed to the delousing drugs azamethiphos and deltamethrin. High transcript levels of the ABCB and ABCC subfamilies were evidenced. Furthermore, SNPs mining was carried out for the ABC proteins sequences, revealing pivotal genomic information. The present study gives a comprehensive transcriptome analysis of ABC proteins from C. rogercresseyi, providing relevant information about transporter roles during ontogeny and in relation to delousing drug responses in salmon lice. This genomic information represents a valuable tool for pest management in the Chilean salmon aquaculture industry.

Structure, Function, and Evolution of Rice Centromeres

Energy Technology Data Exchange (ETDEWEB)

Jiang, Jiming

2010-02-04

The centromere is the most characteristic landmark of eukaryotic chromosomes. Centromeres function as the site for kinetochore assembly and spindle attachment, allowing for the faithful pairing and segregation of sister chromatids during cell division. Characterization of centromeric DNA is not only essential to understand the structure and organization of plant genomes, but it is also a critical step in the development of plant artificial chromosomes. The centromeres of most model eukaryotic species, consist predominantly of long arrays of satellite DNA. Determining the precise DNA boundary of a centromere has proven to be a difficult task in multicellular eukaryotes. We have successfully cloned and sequenced the centromere of rice chromosome 8 (Cen8), representing the first fully sequenced centromere from any multicellular eukaryotes. The functional core of Cen8 spans ~800 kb of DNA, which was determined by chromatin immunoprecipitation (ChIP) using an antibody against the rice centromere-specific H3 histone. We discovered 16 actively transcribed genes distributed throughout the Cen8 region. In addition to Cen8, we have characterized eight additional rice centromeres using the next generation sequencing technology. We discovered four subfamilies of the CRR retrotransposon that is highly enriched in rice centromeres. CRR elements are constitutively transcribed and different CRR subfamilies are differentially processed by RNAi. These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric chromatin.

Rv2477c is an antibiotic-sensitive manganese-dependent ABC-F ATPase in Mycobacterium tuberculosis.

Science.gov (United States)

Daniel, Jaiyanth; Abraham, Liz; Martin, Amanda; Pablo, Xyryl; Reyes, Shelby

2018-01-01

The Rv2477c protein of Mycobacterium tuberculosis (Mtb) belongs to the ATP-binding cassette (ABC) subfamily F that contains proteins with tandem nucleotide-binding domains but lacking transmembrane domains. ABC-F subfamily proteins have been implicated in diverse cellular processes such as translation, antibiotic resistance, cell growth and nutrient sensing. In order to investigate the biochemical characteristics of Rv2477c, we expressed it in Escherichia coli, purified it and characterized its enzymatic functions. We show that Rv2477c displays strong ATPase activity (V max  = 45.5 nmol/mg/min; K m  = 90.5 μM) that is sensitive to orthovanadate. The ATPase activity was maximal in the presence of Mn 2+ at pH 5.2. The Rv2477c protein was also able to hydrolyze GTP, TTP and CTP but at lower rates. Glutamate to glutamine substitutions at amino acid residues 185 and 468 in the two Walker B motifs of Rv2477c severely inhibited its ATPase activity. The antibiotics tetracycline and erythromycin, which target protein translation, were able to inhibit the ATPase activity of Rv2477c. We postulate that Rv2477c could be involved in mycobacterial protein translation and in resistance to tetracyclines and macrolides. This is the first report of the biochemical characterization of an ABC-F subfamily protein in Mtb. Copyright © 2017 Elsevier Inc. All rights reserved.

Structure of the USP15 N-terminal domains: a β-hairpin mediates close association between the DUSP and UBL domains.

Science.gov (United States)

Harper, Stephen; Besong, Tabot M D; Emsley, Jonas; Scott, David J; Dreveny, Ingrid

2011-09-20

Ubiquitin specific protease 15 (USP15) functions in COP9 signalosome mediated regulation of protein degradation and cellular signaling through catalyzing the ubiquitin deconjugation reaction of a discrete number of substrates. It influences the stability of adenomatous polyposis coli, IκBα, caspase-3, and the human papillomavirus type 16 E6. USP15 forms a subfamily with USP4 and USP11 related through a shared presence of N-terminal "domain present in ubiquitin specific proteases" (DUSP) and "ubiquitin-like" (UBL) domains (DU subfamily). Here we report the 1.5 Å resolution crystal structure of the human USP15 N-terminal domains revealing a 80 Å elongated arrangement with the DU domains aligned in tandem. This architecture is generated through formation of a defined interface that is dominated by an intervening β-hairpin structure (DU finger) that engages in an intricate hydrogen-bonding network between the domains. The UBL domain is closely related to ubiquitin among β-grasp folds but is characterized by the presence of longer loop regions and different surface characteristics, indicating that this domain is unlikely to act as ubiquitin mimic. Comparison with the related murine USP4 DUSP-UBL crystal structure reveals that the main DU interdomain contacts are conserved. Analytical ultracentrifugation, small-angle X-ray scattering, and gel filtration experiments revealed that USP15 DU is monomeric in solution. Our data provide a framework to advance study of the structure and function of the DU subfamily. © 2011 American Chemical Society

Field diet of the grasshopper Abracris dilecta Walker (Orthoptera, Acrididae

Directory of Open Access Journals (Sweden)

Carlos Frankl Sperber

1996-01-01

Full Text Available Abracris dilecta Walker, 1870 (Orthoptera, Acrididae, Ommatolampinae ate leafs of at least 14 plant species, in the families Asteraceae, Lamiaceae, Malvales (Sterculiaceae, Tiliaceae or Malvaceae, Poaceae, Fabaceae, Verbenaceae, Aristolochiaceae, Rubiaceae and Melastomataccae. Elephantopus mollis H.B.K. (Asteraceae and Hyptis suaveolens Poit. (Lamiaceae comprised 50% of the diet. The diet breadth of A. dilecta was compared to that of other 11 grasshopper species of the same sub-family, with rarefaction curves. The number of plant species eaten by A. dilecta was greater than that of nine other grasshopper species of the same sub-family (Rhachicreagra spp. but was lower then two others (Microptylopteryx hebardi Rehn, 1905 and Rhachicreagra astytophallus Jago & Rowell, 1981. This results are discussed in view of the broad geographical range and possession of developed wings by A. dilecta, which contrasts with most Ommatolampinae grasshoppers.

A Pan-GTPase Inhibitor as a Molecular Probe.

Directory of Open Access Journals (Sweden)

Lin Hong

Full Text Available Overactive GTPases have often been linked to human diseases. The available inhibitors are limited and have not progressed far in clinical trials. We report here a first-in-class small molecule pan-GTPase inhibitor discovered from a high throughput screening campaign. The compound CID1067700 inhibits multiple GTPases in biochemical, cellular protein and protein interaction, as well as cellular functional assays. In the biochemical and protein interaction assays, representative GTPases from Rho, Ras, and Rab, the three most generic subfamilies of the GTPases, were probed, while in the functional assays, physiological processes regulated by each of the three subfamilies of the GTPases were examined. The chemical functionalities essential for the activity of the compound were identified through structural derivatization. The compound is validated as a useful molecular probe upon which GTPase-targeting inhibitors with drug potentials might be developed.

Moth flies and sand flies (Diptera: Psychodidae in Cretaceous Burmese amber

Directory of Open Access Journals (Sweden)

Frauke Stebner

2015-09-01

Full Text Available One new subfamily, four new genera and 10 new species of Psychodidae are described from Burmese amber which significantly increases our knowledge about this group in the Cretaceous. Protopsychodinae n. subfam. probably represents the oldest known ancestor of modern Psychodinae and includes three species within two genera: Datzia setosa gen. et sp. n., Datzia bispina gen. et sp. n., and Mandalayia beumersorum gen. et sp. n. Sycoracinae and Phlebotominae are represented by two genera each in the studied material, Palaeoparasycorax globosus gen. et sp. n., Palaeoparasycorax suppus gen. et sp. n., Parasycorax simplex sp. n., and Phlebotomites aphoe sp. n. and Phlebotomus vetus sp. n., respectively. Bruchomyiinae is represented by Nemopalpus quadrispiculatus sp. n. Furthermore, one genus of an incertae sedis subfamily, Bamara groehni gen. et sp. n., is described. The systematic positions of the new taxa are discussed.

Endoparasites of horses from the Formiga city, located in center-west region of the state of Minas Gerais, Brazil

Directory of Open Access Journals (Sweden)

Weslen Fabricio Pires Teixeira

2014-12-01

Full Text Available With the aim of studying the endoparasite fauna of horses from the Formiga city, located in center-west region of the state of Minas Gerais, 25 animals that were naturally infected with helminths were evaluated. By means of parasitological necropsies, different endoparasites were found. The subfamily Cyathostominae presented the highest incidence, followed by Trichostrongylus axei, Oxyuris equi, Triodontophorus serratus, Strongyloides westeri, Strongylus edentatus, Habronema muscae, Parascaris equorum, Probstmayria vivipara, Strongylus vulgaris, Gasterophilus nasalis, Anoplocephala magna and Anoplocephala perfoliata. In the present study, if the species Probstmayria vivipara was not considered in the prevalence, the frequency of Cyathostominae was equivalent to 94.85%. The results obtained in this study allowed us to detect and identify different species of helminths in horses, and confirmed the high incidence of nematodes belonging to the subfamily Cyathostominae in the center-west region of Minas Gerais.

Chipmunk parvovirus is distinct from members in the genus Erythrovirus of the family Parvoviridae.

Directory of Open Access Journals (Sweden)

Zhaojun Chen

2010-12-01

Full Text Available The transcription profile of chipmunk parvovirus (ChpPV, a tentative member of the genus Erythrovirus in the subfamily Parvovirinae of the family Parvoviridae, was characterized by transfecting a nearly full-length genome. We found that it is unique from the profiles of human parvovirus B19 and simian parvovirus, the members in the genus Erythrovirus so far characterized, in that the small RNA transcripts were not processed for encoding small non-structural proteins. However, like the large non-structural protein NS1 of the human parvovirus B19, the ChpPV NS1 is a potent inducer of apoptosis. Further phylogenetic analysis of ChpPV with other parvoviruses in the subfamily Parvovirinae indicates that ChpPV is distinct from the members in genus Erythrovirus. Thus, we conclude that ChpPV may represent a new genus in the family Parvoviridae.

Genetic diversity of Bromeliaceae species from the Atlantic Forest.

Science.gov (United States)

Sheu, Y; Cunha-Machado, A S; Gontijo, A B P L; Favoreto, F C; Soares, T B C; Miranda, F D

2017-04-20

The Bromeliaceae family includes a range of species used for many purposes, including ornamental use and use as food, medicine, feed, and fiber. The state of Espírito Santo, Brazil is a center of diversity for this family in the Atlantic Forest. We evaluated the genetic diversity of five populations of the Bromeliaceae family, including specimens of the genera Aechmea, Billbergia (subfamily Bromelioideae), and Pitcairnia (subfamily Pitcairnioidea), all found in the Atlantic Forest and distributed in the state of Espírito Santo. The number of alleles per locus in populations ranged from two to six and the fixation index (F), estimated for some simple sequence repeats in bromeliad populations, was less than zero in all populations. All markers in the Pitcairnia flammea population were in Hardy-Weinberg equilibrium (P Atlantic Forest remnants in the south of Espírito Santo state.

A comparative phylogenetic analysis of full-length mariner elements ...

Indian Academy of Sciences (India)

Unknown

recent study showing non-occurance of inter-subfamily excisions because of .... length shown in our figure is greater because of the gaps introduced to maintain an ... to test the feasibility of transforming silkmoths with a foreign gene of ...

Regulation of basal resistance by a powdery mildew-induced cysteine-rich receptor-like protein kinase in barley

DEFF Research Database (Denmark)

Rayapuram, Channabasavangowda; Jensen, Michael Krogh; Maiser, Fabian

2012-01-01

The receptor-like protein kinases (RLKs) constitute a large and diverse group of proteins controlling numerous plant physiological processes, including development, hormone perception and stress responses. The cysteine-rich RLKs (CRKs) represent a prominent subfamily of transmembrane-anchored RLKs...

Expression-dependent pharmacology of transient receptor potential vanilloid subtype 1 channels in Xenopus laevis oocytes

DEFF Research Database (Denmark)

Rivera-Acevedo, Ricardo E; Pless, Stephan Alexander; Schwarz, Stephan K W

2013-01-01

Transient receptor potential vanilloid subfamily member 1 channels are polymodal sensors of noxious stimuli and integral players in thermosensation, inflammation and pain signaling. It has been shown previously that under prolonged stimulation, these channels show dynamic pore dilation, providing...

Raccoons of North and Middle America

Science.gov (United States)

Goldman, Edward A.; Jackson, Hartley H.T.

1950-01-01

The raccoons, genus Procyon, colloquially known as “coons,” belong to the carnivorous family Procyonidae, which also includes the American genera Nasua, Nasuella, Bassaricyon, and Potos, and the Old World genera Ailurus and Ailuropoda of the subfamily Ailurinae.

Notes on Magnoliaceae with a revision of Pachylarnax and Elmerrillia and the Malesian species of Manglietia and Michelia

NARCIS (Netherlands)

Nooteboom, H.P.

1985-01-01

After the general chapters, mainly based on literature and dealing with wood anatomy, characters of the leaf epidermis and foliar sclereids, embryology and chromosome numbers, phytochemistry, and characters of the fruit, the generic delimitation of subfamily Magnolioideae is discussed. Paramichelia

Karyotypes in Ethiopian Aloe species (Xanthorrhoeaceae: Asphodeloideae)

DEFF Research Database (Denmark)

Fentaw, Eshetu; Dagne, Kifle; Rønsted, Nina

2013-01-01

A cytogenetic survey of 18 species in the succulent-leaved genus Aloe L. (Xanthorrhoeaceae subfamily Asphodeloideae) in Ethiopia was undertaken towards a more complete genetic characterisation of the genus throughout its distribution in Africa, Arabia and Madagascar. Somatic metaphase chromosomes...

EPHA4 is overexpressed but not functionally active in Sezary syndrome

NARCIS (Netherlands)

Hameetman, L; van der Fits, L.; Zoutman, W.H.; Out-Luiting, J.J.; Siegal, G.; de Esch, I.J.P.; Vermeer, M.H.; Tensen, C.P.

2015-01-01

EPHA4 belongs to the largest subfamily of receptor tyrosine kinases. In addition to its function during development, overexpression of EPHA4 in tumors has been correlated with increased proliferation, migration and poor survival. Several genomewide transcription profiling studies have demonstrated

Systematic studies of Bornean Zingiberaceae V. Zingiberoideae of Lambir Hills, Sarawak

NARCIS (Netherlands)

Sakai, S.; Nagamasu, H.

2006-01-01

This paper reports the subfamily Zingiberoideae (Zingiberaceae) of Lambir Hills National Park, Sarawak, Malaysia. Twelve species representing Boesenbergia, Globba, and Zingiber are recorded. Systematic and ecological notes are provided, and the key to the Bornean species of Boesenbergia is updated.

ICTV virus taxonomy profile: Pneumoviridae

NARCIS (Netherlands)

B.K. Rima (Bert); Collins, P. (Peter); Easton, A. (Andrew); R.A.M. Fouchier (Ron); Kurath, G. (Gael); Lamb, R.A. (Robert A.); Lee, B. (Benhur); A. Maisner (Andrea); P.A. Rota (Paul); Wang, L. (Linfa); Lefkowitz, E.J. (Elliot J.); Davison, A.J. (Andrew J.); Simmonds, P. (Peter); Sabanadzovic, S. (Sead); Smith, D.B. (Donald B.); Orton, R.J. (Richard J.); Siddell, S.G. (Stuart G.)

2017-01-01

textabstractThe family Pneumoviridae comprises large enveloped negative-sense RNA viruses. This taxon was formerly a subfamily within the Paramyxoviridae, but was reclassified in 2016 as a family with two genera, Orthopneumovirus and Metapneumovirus. Pneumoviruses infect a range of mammalian

Patterns of interaction specificity of fungus-growing termites and Termitomyces symbionts in South Africa

NARCIS (Netherlands)

Aanen, D.K.; Ros, V.I.D.; Fine Licht, de H.H.; Mitchell, J.; Beer, de Z.W.; Slippers, B.; Rouland-Lefevre, C.; Boomsma, J.J.

2007-01-01

Background Termites of the subfamily Macrotermitinae live in a mutualistic symbiosis with basidiomycete fungi of the genus Termitomyces. Here, we explored interaction specificity in fungus-growing termites using samples from 101 colonies in South-Africa and Senegal, belonging to eight species

Direct multiplex PCR (dmPCR) for the identification of six Phlebotomine sand fly species (Diptera: Psychodidae), including major Leishmania vectors of the Mediterranean

Science.gov (United States)

Sand flies (Diptera: Psychodidae, subfamily Phlebotominae) are haematophagous insects that are known to transmit several anthroponotic and zoonotic diseases. Reliable identification of sand flies at species level is crucial for their surveillance, the detection and spread of their pathogens and the ...

Anatomy, functional morphology, evolutionary ecology and systematics of the invasive gastropod Cipangopaludina japonica (Viviparidae: Bellamyinae)

NARCIS (Netherlands)

Bocxlaer, Van B.; Strong, E.E.

2016-01-01

The anatomy, functional morphology and evolutionary ecology of the Viviparidae, and the subfamily Bellamyinae in particular, are incompletely known. Partly as a result, genealogical relationships within the family remain poorly understood. Because of this lack in knowledge, few informed hypotheses

Activity of pyrrolizidine alkaloids against biofilm formation and Trichomonas vaginalis

Science.gov (United States)

Crotalaria genus belongs to the subfamily Papilionoideae comprising about 600 species spread throughout tropical, neotropical and subtropical regions. In this study, seeds of Crolatalaria pallida were used to the isolation of usaramine, a pyrrolizidine alkaloid. Thus, Pseudomonas aeruginosa and Stap...

Preliminary notes on the decapod larvae of the Arabian Sea

Digital Repository Service at National Institute of Oceanography (India)

Menon, M.K.; Menon, P.G.; Paulinose, V.T.

The note presents some general facts regarding the distribution of some of the larger groups of decapod larvae in the Arabian Sea Their relative numbers and the families and subfamilies, so far as can be recognized, represented within each group...

Direct enzyme assay evidence confirms aldehyde reductase function of Ydr541cp and Ygl039wp from Saccharomyces cerevisiae

Science.gov (United States)

Aldehyde reductase gene ARI1 is a recently characterized member of intermediate subfamily under SDR (short-chain dehydrogenase/reductase) superfamily that revealed mechanisms of in situ detoxification of furfural and HMF for tolerance of Saccharomyces cerevisiae. Uncharacterized open reading frames ...

Genetic and bibliographic information: Abcc9 [GenLibi

Lifescience Database Archive (English)

Full Text Available Abcc9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9 rat Hypertension (MeS...H) Cardiovascular Diseases (C14) > Vascular Diseases (C14.907) > Hypertension (C14.907.489) 04A0394477; 05A0803372 ...

Diversity, ecology and herbivory of hairstreak butterflies (Theclinae) associated with the velvet tree, Miconia calvescens in Costa Rica.

Science.gov (United States)

F.R. Badenes-Pérez; M.A. Alfaro-Alpízar; M.T. Johnson

2010-01-01

Larvae of three species of hairstreak butterflies in the subfamily Theclinae (Lepidoptera: Lycaenidae) were found feeding on developing inflorescences, flower buds, and immature fruits of the velvet tree, (Miconia calvescens) de Candolle (Myrtales: Melastomataceae) in Costa Rica. (Erora opisena) (Druce), (Parrhasius...

Tumour Suppressor Adenomatous Polyposis Coli (APC) localisation is regulated by both Kinesin-1 and Kinesin-2

NARCIS (Netherlands)

Ruane, Peter T; Gumy, Laura F; Bola, Becky; Anderson, Beverley; Wozniak, Marcin J; Hoogenraad, Casper C; Allan, Victoria J

2016-01-01

Microtubules and their associated proteins (MAPs) underpin the polarity of specialised cells. Adenomatous polyposis coli (APC) is one such MAP with a multifunctional agenda that requires precise intracellular localisations. Although APC has been found to associate with kinesin-2 subfamily members,

Molecular and biochemical characterization of a novel intracellular invertase from Aspergillus niger with transfructosylating activity

NARCIS (Netherlands)

Goosen, C.; Yuan, X.L.; Munster, J.M. van; Ram, A.F.J.; Maarel, M.J.E.C. van der; Dijkhuizen, L.

2007-01-01

A novel subfamily of putative intracellular invertase enzymes (glycoside hydrolase family 32) has previously been identified in fungal genomes. Here, we report phylogenetic, molecular, and biochemical characteristics of SucB, one of two novel intracellular invertases identified in Aspergillus niger.

Expression of Nudix hydrolase genes in barley under UV irradiation

Science.gov (United States)

Tanaka, Sayuri; Sugimoto, Manabu; Kihara, Makoto

Seed storage and cultivation should be necessary to self-supply foods when astronauts would stay and investigate during long-term space travel and habitation in the bases on the Moon and Mars. Thought the sunlight is the most importance to plants, both as the ultimate energy source and as an environmental signal regulating growth and development, UV presenting the sunlight can damage many aspects of plant processes at the physiological and DNA level. Especially UV-C, which is eliminated by the stratospheric ozone layer, is suspected to be extremely harmful and give a deadly injury to plants in space. However, the defense mechanism against UV-C irradiation damage in plant cells has not been clear. In this study, we investigated the expression of Nudix hydrolases, which defense plants from biotic / abiotic stress, in barley under UV irradiation. The genes encoding the amino acid sequences, which show homology to those of 28 kinds of Nudix hydrolases in Arabidopsis thaliana, were identified in the barley full-length cDNA library. BLAST analysis showed 14 kinds of barley genes (HvNUDX1-14), which encode the Nudix motif sequence. A phylogenetic tree showed that HvNUDX1, HvNUDX7, HvNUDX9 and HvNUDX11 belonged to the ADP-ribose pyrophosphohydrolase, ADP-sugar pyrophosphohydrolase, NAD(P)H pyrophosphohydrolase and FAD pyrophosphohydrolase subfamilies, respectively, HvNUDX3, HvNUDX6, and HvNUDX8 belonged to the Ap _{n}A pyrophosphohydrolase subfamilies, HvNUDX5 and HvNUDX14 belonged to the coenzyme A pyrophosphohydrolase subfamilies, HvNUDX12 and HvNUDX13 belonged to the Ap _{4}A pyrophosphohydrolase subfamilies. Induction of HvNUDX genes by UV-A (340nm), UV-B (312nm), and UV-C (260nm) were analyzed by quantitative RT-PCR. The results showed that HvNUDX4 was induced by UV-A and UV-B, HvNUDX6 was induced by UV-B and UV-C, and HvNUDX7 and HvNUDX14 were induced by UV-C, significantly. Our results suggest that the response of HvNUDXs to UV irradiation is different by UV

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae).

Science.gov (United States)

Young, Andrew Donovan; Lemmon, Alan R; Skevington, Jeffrey H; Mengual, Ximo; Ståhls, Gunilla; Reemer, Menno; Jordaens, Kurt; Kelso, Scott; Lemmon, Emily Moriarty; Hauser, Martin; De Meyer, Marc; Misof, Bernhard; Wiegmann, Brian M

2016-06-29

Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Anchored hybrid enrichment was successful in producing a robustly supported

Evolutionary conservation and changes in insect TRP channels.

Science.gov (United States)

Matsuura, Hironori; Sokabe, Takaaki; Kohno, Keigo; Tominaga, Makoto; Kadowaki, Tatsuhiko

2009-09-10

TRP (Transient Receptor Potential) channels respond to diverse stimuli and thus function as the primary integrators of varied sensory information. They are also activated by various compounds and secondary messengers to mediate cell-cell interactions as well as to detect changes in the local environment. Their physiological roles have been primarily characterized only in mice and fruit flies, and evolutionary studies are limited. To understand the evolution of insect TRP channels and the mechanisms of integrating sensory inputs in insects, we have identified and compared TRP channel genes in Drosophila melanogaster, Bombyx mori, Tribolium castaneum, Apis mellifera, Nasonia vitripennis, and Pediculus humanus genomes as part of genome sequencing efforts. All the insects examined have 2 TRPV, 1 TRPN, 1 TRPM, 3 TRPC, and 1 TRPML subfamily members, demonstrating that these channels have the ancient origins in insects. The common pattern also suggests that the mechanisms for detecting mechanical and visual stimuli and maintaining lysosomal functions may be evolutionarily well conserved in insects. However, a TRPP channel, the most ancient TRP channel, is missing in B. mori, A. mellifera, and N. vitripennis. Although P. humanus and D. melanogaster contain 4 TRPA subfamily members, the other insects have 5 TRPA subfamily members. T. castaneum, A. mellifera, and N. vitripennis contain TRPA5 channels, which have been specifically retained or gained in Coleoptera and Hymenoptera. Furthermore, TRPA1, which functions for thermotaxis in Drosophila, is missing in A. mellifera and N. vitripennis; however, they have other Hymenoptera-specific TRPA channels (AmHsTRPA and NvHsTRPA). NvHsTRPA expressed in HEK293 cells is activated by temperature increase, demonstrating that HsTRPAs function as novel thermal sensors in Hymenoptera. The total number of insect TRP family members is 13-14, approximately half that of mammalian TRP family members. As shown for mammalian TRP channels, this

Evolutionary conservation and changes in insect TRP channels

Directory of Open Access Journals (Sweden)

Tominaga Makoto

2009-09-01

Full Text Available Abstract Background TRP (Transient Receptor Potential channels respond to diverse stimuli and thus function as the primary integrators of varied sensory information. They are also activated by various compounds and secondary messengers to mediate cell-cell interactions as well as to detect changes in the local environment. Their physiological roles have been primarily characterized only in mice and fruit flies, and evolutionary studies are limited. To understand the evolution of insect TRP channels and the mechanisms of integrating sensory inputs in insects, we have identified and compared TRP channel genes in Drosophila melanogaster, Bombyx mori, Tribolium castaneum, Apis mellifera, Nasonia vitripennis, and Pediculus humanus genomes as part of genome sequencing efforts. Results All the insects examined have 2 TRPV, 1 TRPN, 1 TRPM, 3 TRPC, and 1 TRPML subfamily members, demonstrating that these channels have the ancient origins in insects. The common pattern also suggests that the mechanisms for detecting mechanical and visual stimuli and maintaining lysosomal functions may be evolutionarily well conserved in insects. However, a TRPP channel, the most ancient TRP channel, is missing in B. mori, A. mellifera, and N. vitripennis. Although P. humanus and D. melanogaster contain 4 TRPA subfamily members, the other insects have 5 TRPA subfamily members. T. castaneum, A. mellifera, and N. vitripennis contain TRPA5 channels, which have been specifically retained or gained in Coleoptera and Hymenoptera. Furthermore, TRPA1, which functions for thermotaxis in Drosophila, is missing in A. mellifera and N. vitripennis; however, they have other Hymenoptera-specific TRPA channels (AmHsTRPA and NvHsTRPA. NvHsTRPA expressed in HEK293 cells is activated by temperature increase, demonstrating that HsTRPAs function as novel thermal sensors in Hymenoptera. Conclusion The total number of insect TRP family members is 13-14, approximately half that of mammalian TRP

Key to higher taxa of South American weevils based on adult characters (Coleoptera, Curculionoidea Clave de taxones superiores de gorgojos sudamericanos basada en caracteres de los adultos (Coleoptera, Curculionoidea

Directory of Open Access Journals (Sweden)

ADRIANA E. MARVALDI

2005-03-01

Full Text Available The weevils (Coleoptera: Curculionoidea from South America are currently classified in the following families and subfamilies: Nemonychidae (Rhinorhynchinae, Anthribidae (Anthribinae, Belidae (Belinae and Oxycoryninae, Attelabidae (Attelabinae and Rhynchitinae, Brentidae (Apioninae and Brentinae, Caridae (Carinae and Curculionidae (Erirhininae, Dryophthorinae, Entiminae, Aterpinae, Gonipterinae, Rhythirrininae, Thecesterninae, Eugnominae, Hyperinae, Curculioninae, Cryptorhynchinae, Mesoptiliinae (= Magdalidinae, Molytinae, Baridinae, Lixinae, Conoderinae (= Zygopinae, Cossoninae, Scolytinae and Platypodinae. In the present contribution we bring a dichotomous key for the identification of seven families and 28 subfamilies of Curculionoidea from South America, and for 21 tribes of the highly heterogeneous subfamilies Curculioninae and Molytinae. These tribes are Curculionini Anthonomini, Ceutorhynchini, Derelomini, Otidocephalini, Erodiscini, Camarotini, Piazorhinini, Prionobrachiini, Smicronychini, Rhamphini and Tychiini, within Curculioninae; and Hylobiini, Pissodini, Conotrachelini, Cleogonini, Sternechini, Pacholenini, Cholini, Petalochilini and Amalactini, within Molytinae. Most of them have been classified as subfamilies in traditional schemes. The key is mainly based on external morphological characters, but also includes data on genitalia, mouth parts and other biological features. Definitions and illustrations of diagnostic characters used in the key are providedLos gorgojos (Coleoptera: Curculionoidea de América del Sur se clasifican actualmente en las siguientes familias y subfamilias: Nemonychidae (Rhinorhynchinae, Anthribidae (Anthribinae, Belidae (Belinae y Oxycoryninae, Attelabidae (Attelabinae y Rhynchitinae, Brentidae (Apioninae y Brentinae, Caridae (Carinae y Curculionidae (Erirhininae, Dryophthorinae, Entiminae, Aterpinae, Gonipterinae, Rhythirrininae, Thecesterninae, Eugnominae, Hyperinae, Curculioninae, Cryptorhynchinae

Biometrical studies upon hominoid teeth: the coefficient of variation, sexual dimorphism and questions of phylogenetic relationship.

Science.gov (United States)

Blumenberg, B

1985-01-01

Sexual dimorphism as a function of variation in hominoid tooth metrics has been investigated for four groups of taxa: Recent great apes (two subfamilies), Dryopiths (one subfamily), Ramapiths (one subfamily) and hominids (one family). Gorilla, and to a lesser extent Pan, appear characterized by very high levels of sexual dimorphism and meet several criteria for statistical outliers. Recent great apes are the only group exhibiting consistently high levels of sexual dimorphism. Ramapiths are the only group characterized by low levels of sexual dimorphism and their relative canine length is most similar to Dryopiths. Both Dryopiths and hominids contain taxa with low and intermediate levels of sexual dimorphism. The Gingerich and Shoeninger hypothesis relating coefficients of variation to occlusal complexity is supported. Non-parametric statistics suggest that homogeneity of coefficient of variation profiles over most of the tooth row is characteristic of only the Dryopiths and a composite data set composed of the Dryopith plus Ramapith tooth measurements. Oxnard's model for the multifactorial basis of multiple sexual dimorphisms is also supported. The Dryopith and hominid patterns of sexual dimorphism are similar, an observation that suggests phylogenetic relationship. At the taxonomic level of subfamily or family, sexual dimorphism is a character of cladistic usefulness and possible phylogenetic valence. Assuming that breeding system and sexual dimorphism are functional correlates as many workers suggest, then Ramapithecus sp. China, Sivapithecus indicus and possibly Australopithecus boisei are good candidates for having possessed monogamous breeding/social structures. All Dryopith taxa, S. sivalensis, Sivapithecus sp. China, A. afarensis, Homo habilis and H. erectus emerge as the best candidates for having possessed a polygynous breeding/social structure. No biometrical affinities of Ramapiths with hominids can be demonstrated and some phylogenetic relationship with

The gram-negative bacterium Azotobacter chroococcum NCIMB 8003 employs a new glycoside hydrolase family 70 4,6-α-glucanotransferase enzyme (GtfD) to synthesize a reuteran like polymer from maltodextrins and starch

NARCIS (Netherlands)

Gangoiti, Joana; van Leeuwen, Sander S; Vafiadi, Christina; Dijkhuizen, Lubbert

BACKGROUND: Originally the glycoside hydrolase (GH) family 70 only comprised glucansucrases of lactic acid bacteria which synthesize α-glucan polymers from sucrose. Recently we have identified 2 novel subfamilies of GH70 enzymes represented by the Lactobacillus reuteri 121 GtfB and the

Enteric parvovirus infections of chickens and turkeys

Science.gov (United States)

Chicken and turkey parvoviruses are members of the Parvovirus family. Comparative sequence analysis of their genome structure revealed that they should form a new genus within the vertebrate Parvovirinae subfamily. The first chicken and turkey parvoviruses were identified by electron microscopy duri...

Metabolomic engineering for the microbial production of cartenoids and related products with a focus on the rare C50 carotenoids

NARCIS (Netherlands)

Heider, S.A.E.; Peters-Wendisch, P.; Wendisch, V.F.; Beekwilder, M.J.

2014-01-01

Carotenoids, a subfamily of terpenoids, are yellowtored-colored pigments synthesized by plants, fungi, algae, and bacteria. They are ubiquitous in nature and take over crucial roles in many biological processes as for example photosynthesis, vision, and the quenching of free radicals and singlet

The scIerodactyIid hoIothurians of southern Africa, with the erection ...

African Journals Online (AJOL)

1988-06-15

Jun 15, 1988 ... this basis then they regrouped the various subfamilies of ... dae have retained the typical V-shaped bodies, podia and plated skeletons, while ... sclerodactylid genera (Figure Ib & c), as opposed to the ..... L9.a10 mm J. 11 mm.

Forkhead box O and the control of cellular oxidative stress

NARCIS (Netherlands)

Essers, M.A.G.

2004-01-01

FOXO Forkhead transcription factors are a subfamily of the large superfamily of Forkhead transcription factors, which consists of over 100 different members, expressed in species ranging from yeast to humans. Members of this family of transcription factors have been demonstrated to play important

Lymphocryptovirus phylogeny and the origins of Epstein-Barr virus

DEFF Research Database (Denmark)

Ehlers, Bernhard; Spiess, Katja; Leendertz, Fabian

2010-01-01

Specimens from wild and captive primates were collected and novel members of the genus Lymphocryptovirus (subfamily Gammaherpesvirinae) were searched for utilizing PCR for the DNA polymerase gene. Twenty-one novel viruses were detected. Together with previous findings, more than 50 distinct lymph...

N-lactoyl-amino acids are ubiquitous metabolites that originate from CNDP2-mediated reverse proteolysis of lactate and amino acids

NARCIS (Netherlands)

Jansen, Robert S; Addie, Ruben; Merkx, Remco; Fish, Alexander; Mahakena, Sunny; Bleijerveld, Onno B; Altelaar, Maarten; IJlst, Lodewijk; Wanders, Ronald J; Borst, P; van de Wetering, Koen

2015-01-01

Despite technological advances in metabolomics, large parts of the human metabolome are still unexplored. In an untargeted metabolomics screen aiming to identify substrates of the orphan transporter ATP-binding cassette subfamily C member 5 (ABCC5), we identified a class of mammalian metabolites,

Novel mandibular gland volatiles from Apterostigma ants

DEFF Research Database (Denmark)

Hogan, Conor T.; Jones, Tappey H.; Zhukova, Mariya

2017-01-01

The fungus-farming ants are a well-studied evolutionary radiation within the subfamily Myrmicinae that associate with a web of symbionts that span kingdoms. Members of the Apterostigma pilosum species group cultivate unique basidiomycete fungi belonging to the coral-mushroom family Pterulaceae...

Vitilevumyia, an enigmatic new genus of Stratiomyidae from Fiji (Diptera)

Science.gov (United States)

A new genus of Stratiomyidae, Vitilevumyia gen. nov. (type species, V. bobwoodleyi, sp. nov.) is described from the island of Viti Levu, Fiji. It exhibits an unusual combination of character states, but is tentatively placed in the tribe Prosopochrysini of the subfamily Stratiomyinae. ...

Cellular and substrate adhesion molecules (integrins) and their ligands in cerebral amyloid plaques in Alzheimer's disease

NARCIS (Netherlands)

Eikelenboom, P.; Zhan, S. S.; Kamphorst, W.; van der Valk, P.; Rozemuller, J. M.

1994-01-01

Integrins belonging to different subfamilies can be identified immunohistochemically in cerebral amyloid plaques. Monoclonal antibodies against the VLA family beta 1-integrins show staining of the corona of classical amyloid plaques for beta 1, alpha 3 and alpha 6. Immunostaining reveal also the

Phylogenetic relationships among Maloideae species

Science.gov (United States)

The Maloideae is a highly diverse sub-family of the Rosaceae containing several agronomically important species (Malus sp. and Pyrus sp.) and their wild relatives. Previous phylogenetic work within the group has revealed extensive intergeneric hybridization and polyploidization. In order to develop...

Patterns of interaction specificity of fungus-growing termites and Termitomyces symbionts in South Africa

DEFF Research Database (Denmark)

Aanen, Duur K; Ros, Vera I D; de Fine Licht, Henrik H

2007-01-01

BACKGROUND: Termites of the subfamily Macrotermitinae live in a mutualistic symbiosis with basidiomycete fungi of the genus Termitomyces. Here, we explored interaction specificity in fungus-growing termites using samples from 101 colonies in South-Africa and Senegal, belonging to eight species di...

Brachyura, Grapsidae, Sesarminae

African Journals Online (AJOL)

1986-11-17

Nov 17, 1986 ... subfamily. The diagnostic value of some features of larval morphology is briefly discussed. ... plastic containers filled with sea water (35 %0 salinity) and kept at 20°C ..... podite of the second maxilliped bears no setae. This is a.

Conservation of targeting but divergence in function and quality control of peroxisomal ABC transporters: an analysis using cross-kingdom expression

NARCIS (Netherlands)

Zhang, Xuebin; de Marcos Lousa, Carine; Schutte-Lensink, Nellie; Ofman, Rob; Wanders, Ronald J.; Baldwin, Stephen A.; Baker, Alison; Kemp, Stephan; Theodoulou, Frederica L.

2011-01-01

ABC (ATP-binding cassette) subfamily D transporters are found in all eukaryotic kingdoms and are known to play essential roles in mammals and plants; however, their number, organization and physiological contexts differ. Via cross-kingdom expression experiments, we have explored the conservation of

Brilliant iridescence of Morpho butterfly wing scales is due to both a thin film lower lamina and a multilayered upper lamina

NARCIS (Netherlands)

Giraldo, M A; Stavenga, D G

2016-01-01

Butterflies belonging to the nymphalid subfamily, Morphinae, are famous for their brilliant blue wing coloration and iridescence. These striking optical phenomena are commonly explained as to originate from multilayer reflections by the ridges of the wing scales. Because the lower lamina of the

Giselia arizonica, a new genus and species of mite (Acaria: Tarsonemidae) associated with bark beetles of the genus Pseudopityophthorus (Coleoptera: Scolytidae) in North America

Science.gov (United States)

Wojciech L. Magowski; Evert E. Lindquist; John C. Moser

2005-01-01

A new genus and species of the mite family Tarsonemidae, subfamily Tarsoneminae, is described and illustrated. Its systematic position among genera of Tarsoneminae and its host association with bark beetles of the genus Pseudopityophthorus Swaine, 1918 in North America are briefly discussed.

Vulnerabilities and fisheries impacts : The uncertain future of manta and devil rays

NARCIS (Netherlands)

Croll, Donald A.; Dewar, Heidi; Dulvy, Nicholas K.; Fernando, Daniel; Francis, Malcolm P.; Galván-Magaña, Felipe; Hall, Martin; Heinrichs, Shawn; Marshall, Andrea; Mccauley, Douglas; Newton, Kelly M.; Notarbartolo-Di-Sciara, Giuseppe; O'Malley, Mary; O'Sullivan, John; Poortvliet, Marloes; Roman, Marlon; Stevens, Guy; Tershy, Bernie R.; White, William T.

2016-01-01

Manta and devil rays of the subfamily Mobulinae (mobulids) are rarely studied, large, pelagic elasmobranchs, with all eight of well-evaluated species listed on the IUCN Red List as threatened or near threatened. Mobulids have life history characteristics (matrotrophic reproduction, extremely low

No metabolic effects of mustard allyl-isothiocyanate compared with placebo in men

NARCIS (Netherlands)

Langeveld, Mirjam; Tan, Chong Yew; Soeters, Maarten R.; Virtue, Samuel; Watson, Laura Pe; Murgatroyd, Peter R.; Ambler, Graeme K.; Vidal-Puig, Santiago; Chatterjee, Krishna V.; Vidal-Puig, Antonio

2017-01-01

Background: Induction of nonshivering thermogenesis can be used to influence energy balance to prevent or even treat obesity. The pungent component of mustard, allyl-isothiocyanate (AITC), activates the extreme cold receptor transient receptor potential channel, subfamily A, member 1 and may thus

Several records of Tachinidae (Diptera reared from their hosts in Serbia and Montenegro

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Stanković, S.S.

2014-09-01

Full Text Available During the year 2013 over fifty tachinid flies were reared. Nine tachinid species form two subfamilies were reported for the territory of Serbia and Montenegro. Species Erynniopsis antennata and Phryxe hirta are recorded for the first time in Serbia.

Historical colonization and dispersal limitation supplement climate and topography in shaping species richness of African lizards (Reptilia: Agaminae)

NARCIS (Netherlands)

Kissling, W.D.; Blach-Overgaard, A.; Zwaan, R.E.; Wagner, P.

2016-01-01

To what extent deep-time dispersal limitation shapes present-day biodiversity at broad spatial scales remains elusive. Here, we compiled a continental dataset on the distributions of African lizard species in the reptile subfamily Agaminae (a relatively young, Neogene radiation of agamid lizards

The Y chromosome of the Atelidae family (Platyrrhini): study by chromosome microdissection.

Science.gov (United States)

Gifalli-Iughetti, C; Koiffmann, C P

2009-01-01

In order to study the intergeneric variability of the Y chromosome, we describe the hybridization of the Y chromosome of Brachytelesarachnoides, obtained by microdissection, to metaphases of Atelesbelzebuthmarginatus, Lagothrixlagothricha, and Alouatta male specimens. Brachytelesarachnoides (Atelinae) has 62 chromosomes and a very small Y chromosome. Our results showed that the Brachytelesarachnoides Y chromosome probe hybridized to Lagothrixlagothricha metaphases yielding one hybridization signal on only the tiny Y chromosome, and when hybridized with Atelesbelzebuthmarginatus metaphases it yielded one hybridization signal on two thirds of the small acrocentric Y chromosome. However, no hybridization signal was observed in Alouatta metaphases (subfamily Alouattinae), a closely related genus in the Atelidae family. Furthermore, our data support a close phylogenetic relationship among Brachyteles, Ateles, and Lagothrix and their placement in the Atelinae subfamily, but exclude Alouatta from this group indicating its placement as basal to this group. Copyright 2009 S. Karger AG, Basel.

Molecular Mimicry Regulates ABA Signaling by SnRK2 Kinases and PP2C Phosphatases

International Nuclear Information System (INIS)

Soon, Fen-Fen; Ng, Ley-Moy; Zhou, X. Edward; West, Graham M.; Kovach, Amanda; Tan, M.H. Eileen; Suino-Powell, Kelly M.; He, Yuanzheng; Xu, Yong; Chalmers, Michael J.; Brunzelle, Joseph S.; Zhang, Huiming; Yang, Huaiyu; Jiang, Hualiang; Li, Jun; Yong, Eu-Leong; Cutler, Sean; Zhu, Jian-Kang; Griffin, Patrick R.; Melcher, Karsten; Xu, H. Eric

2012-01-01

Abscisic acid (ABA) is an essential hormone for plants to survive environmental stresses. At the center of the ABA signaling network is a subfamily of type 2C protein phosphatases (PP2Cs), which form exclusive interactions with ABA receptors and subfamily 2 Snfl-related kinase (SnRK2s). Here, we report a SnRK2-PP2C complex structure, which reveals marked similarity in PP2C recognition by SnRK2 and ABA receptors. In the complex, the kinase activation loop docks into the active site of PP2C, while the conserved ABA-sensing tryptophan of PP2C inserts into the kinase catalytic cleft, thus mimicking receptor-PP2C interactions. These structural results provide a simple mechanism that directly couples ABA binding to SnRK2 kinase activation and highlight a new paradigm of kinase-phosphatase regulation through mutual packing of their catalytic sites.

Supersymmetric Extension of Non-Hermitian su(2 Hamiltonian and Supercoherent States

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Omar Cherbal

2010-12-01

Full Text Available A new class of non-Hermitian Hamiltonians with real spectrum, which are written as a real linear combination of su(2 generators in the form H=ωJ_3+αJ_−+βJ_+, α≠β, is analyzed. The metrics which allows the transition to the equivalent Hermitian Hamiltonian is established. A pseudo-Hermitian supersymmetic extension of such Hamiltonians is performed. They correspond to the pseudo-Hermitian supersymmetric systems of the boson-phermion oscillators. We extend the supercoherent states formalism to such supersymmetic systems via the pseudo-unitary supersymmetric displacement operator method. The constructed family of these supercoherent states consists of two dual subfamilies that form a bi-overcomplete and bi-normal system in the boson-phermion Fock space. The states of each subfamily are eigenvectors of the boson annihilation operator and of one of the two phermion lowering operators.

An annotated catalogue of the Iranian Euphorinae, Gnamptodontinae, Helconinae, Hormiinae and Rhysipolinae (Hymenoptera: Braconidae).

Science.gov (United States)

Gadallah, Neveen S; Ghahari, Hassan; Achterberg, Kees Van

2016-01-28

The Iranian species diversity of five braconid subfamilies, Euphorinae (54 species in 16 genera and 8 tribes), Gnamptodontinae (4 species in 1 genus and 1 tribe), Helconinae (9 species in 5 genera and 2 tribes), Hormiinae (8 species in 4 genera and 2 tribe) and Rhysipolinae (3 species in 2 genera) are summarized in this catalogue. A faunistic list is given comprising both local and global distribution of each species under study as well as host records. In the present study ten new records are added to the Iranian fauna: Centistes (Ancylocentrus) ater (Nees), Centistes cuspidatus (Haliday), Meteorus affinis (Wesmael), Meteorus rufus (DeGeer), Microctonus brevicollis (Haliday), Microctonus falciger Ruthe, Peristenus nitidus (Curtis) (Euphorinae), Aspicolpus carinator (Nees), Diospilus capito (Nees) and Diospilus productus Marshall (Helconinae s.l.). Euphorus pseudomitis Hedwig, 1957 is transferred to the subfamily Hormiinae and Hormisca pseudomitis (Hedwig, 1957) is a new combination.

Estudo morfométrico do gênero Panstrongylus Berg, 1879 (Hemiptera, Reduviidae, Triatominae Morphometric study of the genus Panstrongylus Berg, 1879 (Hemiptera, Reduviidae, Triatominae

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Carolina Magalhães dos Santos

2003-10-01

Full Text Available The subfamily Triatominae is actually represented by 137 species distributed among 6 tribes and 19 genera. Within this subfamily, the genus Panstrongylus, Berg 1879, is composed by 13 species widespread in sylvatic, peridomestic, and domestic habitats of Neotropical regions. These species are vectors of Chagas disease and consequently are found associated with its main hosts, such as birds and mammals. Interest in species of this genus has been increasing in the last few years. Reports of several authors indicate these Triatominae to invade and colonize houses, increasing their epidemiological significance. Morphometry was used in this study to investigate correlations among possible closely related species. We measured 224 specimens among 13 species through a set of metric variables of the head. The results indicated that the genus Panstrongylus seems to be homogeneous since 10 of the 14 species were shown to be closely related.

La tribu Pycnopalpini n. trib. (Orthoptera, Tettigonioidea, Phaneropteridae: segunda contribución a la organización supragenérica de los faneropterinos neotropicales

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Cadena–Castañeda, O. J.

2014-12-01

Full Text Available The tribe Pycnopalpini n. trib. (Orthoptera, Tettigonioidea, Phaneropteridae: second contribution to neotropical Phaneropterinae The new tribe Pycnopalpini is proposed, based on morphological similarity among the genera Hetaira, Pycnopalpa, Topana (Pycnopalpina n. subtr., Dolichocercus, Oxyprorella, Theia, and TheiellaTheia unicolor, Theia bifurcata n. sp., Theiella amazonica n. sp., Theiella andina n. sp., and D. santanderensis n. sp. from Colombia, and D. costaricensis n. sp. from Costa Rica. Hetaira (Atopana morona and Hetaira (Atopana varia are recorded from the Colombian Amazon, where both species seem to occur sympatrically. Theia peruviana n. comb. is also recorded from the Colombian Amazon, where it seems to occur sympatrically with T. bifurcata. The paper contains additional new combinations, and Oxyprorella gregoirea syn. n. is a new synonym for Insara bolivari. This contribution reconsiders the neotropical subfamily Phaneropterinae, aiming to establish the limits of the tribes and genera of this subfamily.

Cell-based lipid flippase assay employing fluorescent lipid derivatives

DEFF Research Database (Denmark)

Jensen, Maria Stumph; Costa, Sara; Günther-Pomorski, Thomas

2016-01-01

P-type ATPases in the P4 subfamily (P4-ATPases) are transmembrane proteins unique for eukaryotes that act as lipid flippases, i.e., to translocate phospholipids from the exofacial to the cytofacial monolayer of cellular membranes. While initially characterized as aminophospholipid translocases, s...... flippase activities in the plasma membrane of cells, using yeast as an example.......P-type ATPases in the P4 subfamily (P4-ATPases) are transmembrane proteins unique for eukaryotes that act as lipid flippases, i.e., to translocate phospholipids from the exofacial to the cytofacial monolayer of cellular membranes. While initially characterized as aminophospholipid translocases......, studies of individual P4-ATPase family members from fungi, plants, and animals show that P4-ATPases differ in their substrate specificities and mediate transport of a broader range of lipid substrates. Here, we describe an assay based on fluorescent lipid derivatives to monitor and characterize lipid...

Molecular Mimicry Regulates ABA Signaling by SnRK2 Kinases and PP2C Phosphatases

Energy Technology Data Exchange (ETDEWEB)

Soon, Fen-Fen; Ng, Ley-Moy; Zhou, X. Edward; West, Graham M.; Kovach, Amanda; Tan, M.H. Eileen; Suino-Powell, Kelly M.; He, Yuanzheng; Xu, Yong; Chalmers, Michael J.; Brunzelle, Joseph S.; Zhang, Huiming; Yang, Huaiyu; Jiang, Hualiang; Li, Jun; Yong, Eu-Leong; Cutler, Sean; Zhu, Jian-Kang; Griffin, Patrick R.; Melcher, Karsten; Xu, H. Eric (Van Andel); (Scripps); (NWU); (Purdue); (UCR); (Chinese Aca. Sci.); (NU Singapore)

2014-10-02

Abscisic acid (ABA) is an essential hormone for plants to survive environmental stresses. At the center of the ABA signaling network is a subfamily of type 2C protein phosphatases (PP2Cs), which form exclusive interactions with ABA receptors and subfamily 2 Snfl-related kinase (SnRK2s). Here, we report a SnRK2-PP2C complex structure, which reveals marked similarity in PP2C recognition by SnRK2 and ABA receptors. In the complex, the kinase activation loop docks into the active site of PP2C, while the conserved ABA-sensing tryptophan of PP2C inserts into the kinase catalytic cleft, thus mimicking receptor-PP2C interactions. These structural results provide a simple mechanism that directly couples ABA binding to SnRK2 kinase activation and highlight a new paradigm of kinase-phosphatase regulation through mutual packing of their catalytic sites.

A classification scheme for alternative oxidases reveals the taxonomic distribution and evolutionary history of the enzyme in angiosperms.

Science.gov (United States)

Costa, José Hélio; McDonald, Allison E; Arnholdt-Schmitt, Birgit; Fernandes de Melo, Dirce

2014-11-01

A classification scheme based on protein phylogenies and sequence harmony method was used to clarify the taxonomic distribution and evolutionary history of the alternative oxidase (AOX) in angiosperms. A large data set analyses showed that AOX1 and AOX2 subfamilies were distributed into 4 phylogenetic clades: AOX1a-c/1e, AOX1d, AOX2a-c and AOX2d. High diversity in AOX family compositions was found. While the AOX2 subfamily was not detected in monocots, the AOX1 subfamily has expanded (AOX1a-e) in the large majority of these plants. In addition, Poales AOX1b and 1d were orthologous to eudicots AOX1d and then renamed as AOX1d1 and 1d2. AOX1 or AOX2 losses were detected in some eudicot plants. Several AOX2 duplications (AOX2a-c) were identified in eudicot species, mainly in the asterids. The AOX2b originally identified in eudicots in the Fabales order (soybean, cowpea) was divergent from AOX2a-c showing some specific amino acids with AOX1d and then it was renamed as AOX2d. AOX1d and AOX2d seem to be stress-responsive, facultative and mutually exclusive among species suggesting a complementary role with an AOX1(a) in stress conditions. Based on the data collected, we present a model for the evolutionary history of AOX in angiosperms and highlight specific areas where further research would be most beneficial. Copyright © 2014 Elsevier B.V. All rights reserved.

Atrial natriuretic factor receptor guanylate cyclase, ANF-RGC, transduces two independent signals, ANF and Ca2+

Directory of Open Access Journals (Sweden)

Teresa eDuda

2014-03-01

Full Text Available Atrial natriuretic factor receptor guanylate cyclase, ANF-RGC, was the first discovered member of the mammalian membrane guanylate cyclase family. The hallmark feature of the family is that a single protein contains both the site for recognition of the regulatory signal and the ability to transduce it into the production of the second messenger, cyclic GMP. For over two decades, the family has been classified into two subfamilies, the hormone receptor subfamily with ANF-RGC being its paramount member, and the Ca2+ modulated subfamily, which includes the rod outer segment guanylate cyclases, ROS-GC1 and 2, and the olfactory neuroepithelial guanylate cyclase, ONE-GC. ANF-RGC is the receptor and the signal transducer of the most hypotensive hormones, atrial natriuretic factor (ANF and B-type natriuretic peptide (BNP. After binding these hormones at the extracellular domain it, at its intracellular domain, signals activation of the C-terminal catalytic module and accelerates the production of cyclic GMP. Cyclic GMP then serves the second messenger role in biological responses of ANF and BNP such as natriuresis, diuresis, vasorelaxation and anti-proliferation. Very recently another modus operandi for ANF-RGC was revealed. Its crux is that ANF-RGC activity is also regulated by Ca2+. The Ca2+ sensor neurocalcin  mediates this signaling mechanism. Strikingly, the Ca2+ and ANF signaling mechanisms employ separate structural motifs of ANF-RGC in modulating its core catalytic domain in accelerating the production of cyclic GMP. In this review the biochemistry and physiology of these mechanisms with emphasis on cardiovascular regulation will be discussed.

Genome-wide analysis of ATP-binding cassette (ABC) transporters in the sweetpotato whitefly, Bemisia tabaci.

Science.gov (United States)

Tian, Lixia; Song, Tianxue; He, Rongjun; Zeng, Yang; Xie, Wen; Wu, Qingjun; Wang, Shaoli; Zhou, Xuguo; Zhang, Youjun

2017-04-26

ABC transporter superfamily is one of the largest and ubiquitous groups of proteins. Because of their role in detoxification, insect ABC transporters have gained more attention in recent years. In this study, we annotated ABC transporters from a newly sequenced sweetpotato whitefly genome. Bemisia tabaci Q biotype is an emerging global invasive species that has caused extensive damages to field crops as well as ornamental plants. A total of 55 ABC transporters containing all eight described subfamilies (A to H) were identified in the B. tabaci Q genome, including 8 ABCAs, 3 ABCBs, 6 ABCCs, 2 ABCDs, 1 ABCE, 3 ABCFs, 23 ABCGs and 9 ABCHs. In comparison to other species, subfamilies G and H in both phloem- and blood-sucking arthropods are expanded. The temporal expression profiles of these 55 ABC transporters throughout B. tabaci developmental stages and their responses to imidacloprid, a neonicotinoid insecticide, were investigated using RNA-seq analysis. Furthermore, the mRNA expression of 24 ABC transporters (44% of the total) representing all eight subfamilies was confirmed by the quantitative real-time PCR (RT-qPCR). Furthermore, mRNA expression levels estimated by RT-qPCR and RNA-seq analyses were significantly correlated (r = 0.684, p analysis of the entire repertoire of ABC transporters in B. tabaci. The identification of these ABC transporters, their temporal expression profiles during B. tabaci development, and their response to a neonicotinoid insecticide lay the foundation for functional genomic understanding of their contribution to the invasiveness of B. tabaci.

Evidence for distinct roles of the SEPALLATA gene LEAFY HULL STERILE1 in Eleusine indica and Megathyrsus maximus (Poaceae).

Science.gov (United States)

Reinheimer, Renata; Malcomber, Simon T; Kellogg, Elizabeth A

2006-01-01

LEAFY HULL STERILE1 (LHS1) is an MIKC-type MADS-box gene in the SEPALLATA class. Expression patterns of LHS1 homologs vary among species of grasses, and may be involved in determining palea and lemma morphology, specifying the terminal floret of the spikelet, and sex determination. Here we present LHS1 expression data from Eleusine indica (subfamily Chloridoideae) and Megathyrsus maximus (subfamily Panicoideae) to provide further insights into the hypothesized roles of the gene. E. indica has spikelets with three to eight florets that mature acropetally; E. indica LHS1 (EiLHS1) is expressed in the palea and lemma of all florets. In contrast, M. maximus has spikelets with two florets that mature basipetally; M. maximus LHS1 (MmLHS1) is expressed in the palea and lemma of the distal floret only. These data are consistent with the hypothesis that LHS1 plays a role in determining palea and lemma morphology and specifies the terminal floret of basipetally maturing grass spikelets. However, LHS1 expression does not correlate with floret sex expression; MmLHS1 is restricted to the bisexual distal floret, whereas EiLHS1 is expressed in both sterile and bisexual floret meristems. Phylogenetic analyses reconstruct a complex pattern of LHS1 expression evolution in grasses. LHS1 expression within the gynoecium has apparently been lost twice, once before diversification of a major clade within tribe Paniceae, and once in subfamily Chloridoideae. These data suggest that LHS1 has multiple roles during spikelet development and may have played a role in the diversification of spikelet morphology.

Epidemiology, disease and control of infections in ruminants by herpesviruses - an overview : review article

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J.R. Patel

2008-05-01

Full Text Available There are at least 16 recognised herpesviruses that naturally infect cattle, sheep, goats and various species of deer and antelopes. Six of the viruses are recognised as distinct alphaherpesviruses and 9 as gammaherpesviruses. Buffalo herpesvirus (BflHV and ovine herpesvirus-1 (OvHV-1 remain officially unclassified. The prevalence of ruminant herpesviruses varies from worldwide to geographically restricted in distribution. Viruses in both subfamilies Alphaherpesvirinae and Gammaherpesvirinae cause mild to moderate and severe disease in respective natural or secondary ruminant hosts. Accordingly, the economic and ecological impact of the viruses is also variable. The molecular characteristics of some members have been investigated in detail. This has led to the identification of virulence-associated genes and construction of deletion mutants and recombinant viruses. Some of the latter have been developed as commercial vaccines. This paper aims to give an overview of the epidemiology and pathogenesis of infection by these viruses, immuno-prophylaxis and mechanisms of recovery from infection. Since there are 128 ruminant species in the family Bovidae, it is likely that some herpesviruses remain undiscovered. We conclude that currently known ruminant alphaherpesviruses occur only in their natural hosts and do not cross stably into other ruminant species. By contrast, gammaherpesviruses have a much broader host range as evidenced by the fact that antibodies reactive to alcelaphine herpesvirus type 1 have been detected in 4 subfamilies in the family Bovidae, namely Alcelaphinae, Hippotraginae, Ovibovinae and Caprinae. New gammaherpesviruses within these subfamilies are likely to be discovered in the future.

Generic diversity of ants (Himenopteros: Formicidae in forest set, forest border and areas cultivated three Communities of the Municipality of Coripata, Nor Yungas Department of La Paz, Bolivia

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Mamani-Mamani Beatriz

2012-08-01

Full Text Available The biodiversity is the variety of all the vegetables, animals and the microorganisms that end up coexisting and interaction inside an ecosystem to be interrelated to each other. The ants represent the biggest abundance inside the insects. The family Formicidae is characterized by the importance that has in the natural ecosystems and for the variety of ecological functions that you/they complete, due to the association with many plants and animals. They have a great variability in the feeding and they use diverse nidificación forms; however they are very scarce the carried out studies. The present investigation was carried out in the municipality of Coripata, where the family Formicidae showed bigger abundance and wealth among habitats. For that they settled the 5 traps of having fallen by place (Altuspata, Choro and Alto Choro in three types of different habitats (forest, forest border and cultivation during 12 months. 15026 individuals were distributed in 6 subfamilies with 26 goods and 46 species y/o morfoespecies found in total. This shows that it exists a great wealth and abundance of ants in this ecosystem. The subfamilies Ecitoninae showed a bigger number of individuals for the habit form that you/they have of being depredators and nomadic. The biggest wealth and abundance of ants was identified in the area of forest of the place Altuspata. Inside the subfamilies Ecitoninae the species Labidus spininoides and Labidus praedator presented bigger number, and with regard to the places one has similarity as for the quantity of individuals.

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

Science.gov (United States)

Saski, Christopher; Lee, Seung-Bum; Fjellheim, Siri; Guda, Chittibabu; Jansen, Robert K.; Luo, Hong; Tomkins, Jeffrey; Rognli, Odd Arne; Clarke, Jihong Liu

2009-01-01

Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19–37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C–U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae. PMID:17534593

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

Science.gov (United States)

2013-01-01

Background The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. Results The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. Conclusions We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes. PMID:23627680

Phylogenetic relationships and evolution of growth form in Cactaceae (Caryophyllales, Eudicotyledoneae).

Science.gov (United States)

Hernández-Hernández, Tania; Hernández, Héctor M; De-Nova, J Arturo; Puente, Raul; Eguiarte, Luis E; Magallón, Susana

2011-01-01

Cactaceae is one of the most charismatic plant families because of the extreme succulence and outstanding diversity of growth forms of its members. Although cacti are conspicuous elements of arid ecosystems in the New World and are model systems for ecological and anatomical studies, the high morphological convergence and scarcity of phenotypic synapomorphies make the evolutionary relationships and trends among lineages difficult to understand. We performed phylogenetic analyses implementing parsimony ratchet and likelihood methods, using a concatenated matrix with 6148 bp of plastid and nuclear markers (trnK/matK, matK, trnL-trnF, rpl16, and ppc). We included 224 species representing approximately 85% of the family's genera. Likelihood methods were used to perform an ancestral character reconstruction within Cactoideae, the richest subfamily in terms of morphological diversity and species number, to evaluate possible growth form evolutionary trends. Our phylogenetic results support previous studies showing the paraphyly of subfamily Pereskioideae and the monophyly of subfamilies Opuntioideae and Cactoideae. After the early divergence of Blossfeldia, Cactoideae splits into two clades: Cacteae, including North American globose and barrel-shaped members, and core Cactoideae, including the largest diversity of growth forms distributed throughout the American continent. Para- or polyphyly is persistent in different parts of the phylogeny. Main Cactoideae clades were found to have different ancestral growth forms, and convergence toward globose, arborescent, or columnar forms occurred in different lineages. Our study enabled us to provide a detailed hypothesis of relationships among cacti lineages and represents the most complete general phylogenetic framework available to understand evolutionary trends within Cactaceae.

Genome-wide identification, sequence characterization, and protein-protein interaction properties of DDB1 (damaged DNA binding protein-1)-binding WD40-repeat family members in Solanum lycopersicum.

Science.gov (United States)

Zhu, Yunye; Huang, Shengxiong; Miao, Min; Tang, Xiaofeng; Yue, Junyang; Wang, Wenjie; Liu, Yongsheng

2015-06-01

One hundred DDB1 (damaged DNA binding protein-1)-binding WD40-repeat domain (DWD) family genes were identified in the S. lycopersicum genome. The DWD genes encode proteins presumably functioning as the substrate recognition subunits of the cullin4-ring ubiquitin E3 ligase complex. These findings provide candidate genes and a research platform for further gene functionality and molecular breeding study. A subclass of DDB1 (damaged DNA binding protein-1)-binding WD40-repeat domain (DWD) family proteins has been demonstrated to function as the substrate recognition subunits of the cullin4-ring ubiquitin E3 ligase complex. However, little information is available about the cognate subfamily genes in tomato (S. lycopersicum). In this study, based on the recently released tomato genome sequences, 100 tomato genes encoding DWD proteins that potentially interact with DDB1 were identified and characterized, including analyses of the detailed annotations, chromosome locations and compositions of conserved amino acid domains. In addition, a phylogenetic tree, which comprises of three main groups, of the subfamily genes was constructed. The physical interaction between tomato DDB1 and 14 representative DWD proteins was determined by yeast two-hybrid and co-immunoprecipitation assays. The subcellular localization of these 14 representative DWD proteins was determined. Six of them were localized in both nucleus and cytoplasm, seven proteins exclusively in cytoplasm, and one protein either in nucleus and cytoplasm, or exclusively in cytoplasm. Comparative genomic analysis demonstrated that the expansion of these subfamily members in tomato predominantly resulted from two whole-genome triplication events in the evolution history.

Six subgroups and extensive recent duplications characterize the evolution of the eukaryotic tubulin protein family.

Science.gov (United States)

Findeisen, Peggy; Mühlhausen, Stefanie; Dempewolf, Silke; Hertzog, Jonny; Zietlow, Alexander; Carlomagno, Teresa; Kollmar, Martin

2014-08-27

Tubulins belong to the most abundant proteins in eukaryotes providing the backbone for many cellular substructures like the mitotic and meiotic spindles, the intracellular cytoskeletal network, and the axonemes of cilia and flagella. Homologs have even been reported for archaea and bacteria. However, a taxonomically broad and whole-genome-based analysis of the tubulin protein family has never been performed, and thus, the number of subfamilies, their taxonomic distribution, and the exact grouping of the supposed archaeal and bacterial homologs are unknown. Here, we present the analysis of 3,524 tubulins from 504 species. The tubulins formed six major subfamilies, α to ζ. Species of all major kingdoms of the eukaryotes encode members of these subfamilies implying that they must have already been present in the last common eukaryotic ancestor. The proposed archaeal homologs grouped together with the bacterial TubZ proteins as sister clade to the FtsZ proteins indicating that tubulins are unique to eukaryotes. Most species contained α- and/or β-tubulin gene duplicates resulting from recent branch- and species-specific duplication events. This shows that tubulins cannot be used for constructing species phylogenies without resolving their ortholog-paralog relationships. The many gene duplicates and also the independent loss of the δ-, ε-, or ζ-tubulins, which have been shown to be part of the triplet microtubules in basal bodies, suggest that tubulins can functionally substitute each other. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Short communications: Calls of three species of arthroleptid frogs ...

African Journals Online (AJOL)

The calls of three anuran species in the family Arthroleptidae in the sub-family Astylosterminae from Equatorial Guinea are described including information on calling behaviour. For each species, we present a characteristic audiospectrogram and oscillogram. We also provide numerical information about the spectral and ...

A new genus of Tetratermini (Hymenoptera: Braconidae: Lysiterminae) parasitic on grasshoppers (Gryllacrididae)

NARCIS (Netherlands)

Achterberg, van C.; Steiner, H.

1996-01-01

The new genus Katytermus from Malaysia (type species: Katytermus palmicola spec. nov.) is described and illustrated. The new genus belongs to a new tribe, Tetratermini, of the subfamily Lysiterminae. The type species has been reared as a gregarious endoparasite of a "katydid" longhorn grasshopper

Influence of host and geographic locale on the distribution of Colletotrichum cereale lineages

Science.gov (United States)

Colletotrichum cereale is an ascomycete inhabitant of cool-season grasses of the Pooideae subfamily. The fungus has increased in frequency over the past decade as a destructive pathogen of Poa annua and Agrostis stolonifera cultivated as turfgrass. DNA fingerprinting has revealed two distinct C. c...

The occurrence and evolution of nectar extraction apparatus among Hymenoptera ‘Symphyta'. Jervis, M. & Vilhelmsen, L

DEFF Research Database (Denmark)

Vilhelmsen, Lars

2000-01-01

Takeuchi). CNEA of some type or other has arisen at least twice within the family Tenthredinidae and at least twice within the pergid subfamily Euryinae. Evolutionary parallelism in CNEA structure has occurred between the basal, ‘symphytan', hymenopteran lineages and the Apocrita, a phenomenon hitherto...

Phylogenetic analysis of Thai oyster (Ostreidae) based on partial sequences of the mitochondrial 16S rDNA gene

DEFF Research Database (Denmark)

Bussarawit, Somchai; Gravlund, Peter; Glenner, Henrik

2006-01-01

Ten oyster species of the family Ostreidae (Subfamilies Crassostreinae and Lophinae) from Thailand were studied using morphological data and mitochondrial 16S rDNA gene sequences. Additional sequence data from five specimens of Ostreidae and one specimen of Tridacna gigas were downloaded from Gen...

Phylogenetic analysis of six WRKY transcription factor loci across the spiny cocosoid palm subtribes Bactridinae and Elaeidinae (Areceaceae, Cocoseae),and comparison of several gene tree/species tree reconciliation approaches

Science.gov (United States)

The Cocoseae is one of 13 tribes of Arecaceae subfamily Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera, the coconut, and African oil palm (Elaeis guineensis). Using seven single copy WRKY transcription factor g...

What do we know about the phylogeny of the semi-aquatic bugs (Hemiptera: Heteroptera: Gerromorpha)?

DEFF Research Database (Denmark)

Damgaard, Jakob

2012-01-01

The present study summarizes knowledge about phylogenetic relationships of the heteropteran infraorder Gerromorpha. A phylogeny for all families and subfamilies, and for all genera but those assigned to the two most diverse families, Veliidae and Gerridae, is compiled from the many studies by the...

A new genus of Blacinae (Hymenoptera: Braconidae)

Science.gov (United States)

Lester P. Gibson

1977-01-01

A new genus, Canalicephalus, of the subfamily Blacinae is described along with 4 new species, C. orientalis from Borneo, C. novus from New Guinea, and C. bakeri and C. mindanao, both from the Philippines. Keys are included to separate these 2 genera and the 4...

NCBI nr-aa BLAST: CBRC-CFAM-21-0168 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-CFAM-21-0168 ref|NP_001077100.1| cOR52N9 olfactory receptor family 52 subfamily N-like [Canis lupus... familiaris] gb|ABO36681.1| 52N9 olfactory receptor protein [Canis lupus familiaris] NP_001077100.1 0.0 99% ...

List of the primary types of social wasps (Hymenoptera: Vespidae) deposited in the Nationaal Natuurhistorisch Museum, Leiden, and the Zoölogisch Museum, Amsterdam

NARCIS (Netherlands)

Kojima, J.; Achterberg, van C.

1997-01-01

The primary types of social wasp subfamilies Vespinae, Polistinae and Stenogastrinae housed in the Nationaal Natuurhistorisch Museum in Leiden and the Zoölogisch Museum in Amsterdam are listed. Their complete label data are given unless they are available elsewhere. Lectotypes of Polistes snelleni

Pyrus

Science.gov (United States)

Pear species belong to the genus Pyrus, the subtribe Pyrinae, the subfamily Maloideae (Pomoideae) in the family Rosaceae. There are at least 26 widely recognized primary species and 10 naturally occurring interspecific hybrid taxa, which are distributed in Europe, temperate Asia and mountainous are...

varlUS and M .

African Journals Online (AJOL)

reduction in mean annual temperature (Meester 1963). However, Myosorex is grouped with the crocidurines on account of its unpigmented teeth and continuous articular facets on the mandibular condyle (Repenning 1967). Baxter, Goulden & Meester (1979) have shown that subfamilial differences in metabolic rates of ...

Drug trafficking in mice: In vivo functions of OATP uptake and ABC efflux transporters

NARCIS (Netherlands)

Iusuf, D.

2013-01-01

In recent years, there has been increasing attention for drug uptake transporters of the Organic Anion-Transporting Polypeptide (human OATP, mouse Oatp, gene names SLCO, Slco) superfamily. Especially the OATP1A and OATP1B subfamilies turn out to have important physiological and pharmacological

Na+-independent, nifedipine-resistant rat afferent arteriolar Ca2+ responses to noradrenaline

DEFF Research Database (Denmark)

Salomonsson, Max; Braunstein, Thomas Hartig; von Holstein-Rathlou, Niels-Henrik

2010-01-01

Abstract Aim: In rat afferent arterioles we investigated the role of Na(+) entry in noradrenaline (NA)-induced depolarization and voltage-dependent Ca(2+) entry together with the importance of the transient receptor potential channel (TRPC) subfamily for non-voltage-dependent Ca(2+) entry. Methods...

Biallelic Variants in OTUD6B Cause an Intellectual Disability Syndrome Associated with Seizures and Dysmorphic Features

DEFF Research Database (Denmark)

Santiago-Sim, Teresa; Burrage, Lindsay C; Ebstein, Frédéric

2017-01-01

regulators of the ubiquitin system. OTUD6B encodes a member of the ovarian tumor domain (OTU)-containing subfamily of deubiquitinating enzymes. Herein, we report biallelic pathogenic variants in OTUD6B in 12 individuals from 6 independent families with an intellectual disability syndrome associated...

Monohedotrochus capitolii, a new genus and species of solitary azooxanthellate coral (Scleractinia, Caryophylliidae) from southern Brazil

NARCIS (Netherlands)

Kitahara, M.V.; Cairns, S.D.

2005-01-01

A new genus and species of azooxanthellate solitary coral, Monohedotrochus capitolii, are described in the subfamily Caryophylliinae, based on 42 specimens, most collected off Santa Catarina and Rio Grande do Sul states, southern Brazil. The new genus is characterized by being solitary and attached,

Rational design of avian metapneumovirus live attenuated vaccines by inhibiting viral messenger RNA cap methyltransferase

Science.gov (United States)

Avian metapneumovirus (aMPV), also known as avian pneumovirus or turkey rhinotracheitis, is a non-segmented negative-sense RNA virus belonging to the family of Paramyxoviridae, the subfamily Pneumovirinae, and the genus Metapneumovirus. aMPV is the causative agent of respiratory tract infection and ...

Farnesoid X Receptor Activation Promotes Hepatic Amino Acid Catabolism and Ammonium Clearance in Mice

NARCIS (Netherlands)

Massafra, Vittoria; Milona, Alexandra; Vos, Harmjan R; Ramos, Rúben J J; Gerrits, Johan; Willemsen, Ellen C L; Ramos Pittol, José M; Ijssennagger, Noortje; Houweling, Martin; Prinsen, Hubertus C M T; Verhoeven-Duif, Nanda M; Burgering, Boudewijn M T; van Mil, Saskia W C

2017-01-01

BACKGROUND & AIMS: The nuclear receptor subfamily 1 group H member 4 (NR1H4 or farnesoid X receptor [FXR]) regulates bile acid synthesis, transport, and catabolism. FXR also regulates postprandial lipid and glucose metabolism. We performed quantitative proteomic analyses of liver tissues from mice

Taxonomic revision of the spider family Penestomidae (Araneae, Entelegynae)

NARCIS (Netherlands)

Miller, J.A.; Griswold, C.E.; Haddad, C.R.

2010-01-01

Conflicting character evidence and a scarcity of male specimens has historically made placement of the spider subfamily Penestominae Simon problematic. The Penestominae was recently removed from the family Eresidae and promoted to family rank based on the results of a molecular phylogenetic study; a