scholarly journals Dissecting Transcription Factor-Target Interaction in Bovine Coronavirus Infection

2020 ◽  
Vol 8 (9) ◽  
pp. 1323
Author(s):  
Olanrewaju B. Morenikeji ◽  
Ellis Strutton ◽  
Madeleine Wallace ◽  
Kahleel Bernard ◽  
Elaine Yip ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Phylogenetic Analyses ◽  
Bovine Coronavirus ◽  
Cattle Industry ◽  
Target Interaction ◽  
New Information ◽  
Literature Searches ◽  
Transcription Factor Target ◽  
Functional Analyses ◽  
Significant Disease

Coronaviruses are RNA viruses that cause significant disease within many species, including cattle. Bovine coronavirus (BCoV) infects cattle and wild ruminants, both as a respiratory and enteric pathogen, and possesses a significant economic threat to the cattle industry. Transcription factors are proteins that activate or inhibit transcription through DNA binding and have become new targets for disease therapies. This study utilized in silico tools to identify potential transcription factors that can serve as biomarkers for regulation of BCoV pathogenesis in cattle, both for testing and treatment. A total of 11 genes were identified as significantly expressed during BCoV infection through literature searches and functional analyses. Eleven transcription factors were predicted to target those genes (AREB6, YY1, LMO2, C-Rel, NKX2-5, E47, RORAlpha1, HLF, E4BP4, ARNT, CREB). Function, network, and phylogenetic analyses established the significance of many transcription factors within the immune response. This study establishes new information on the transcription factors and genes related to host-pathogen interactome in BCoV infection, particularly transcription factors YY1, AREB6, LMO2, and NKX2, which appear to have strong potential as diagnostic markers, and YY1 as a potential target for drug therapies.

scholarly journals Forecasting Cattle Prices in the Presence of Structural Change

1992 ◽  
Vol 24 (2) ◽  
pp. 11-22 ◽  
Author(s):  
Barry K. Goodwin
Keyword(s):  
Structural Change ◽  
A Priori ◽  
Arima Model ◽  
Var Model ◽  
Impulse Response Functions ◽  
Cattle Industry ◽  
Vector Autoregressive ◽  
Economic Relationships ◽  
New Information ◽  
Out Of Sample

AbstractRecent empirical research and developments in the cattle industry suggest several reasons to suspect structural change in economic relationships determining cattle prices. Standard forecasting models may ignore structural change and may produce biased and misleading forecasts. Vector autoregressive (VAR) models that allow parameters to vary with time are used to forecast quarterly cattle prices. The VAR procedures are flexible in that they allow the identification of structural change that begins at an a priori unknown point and occurs gradually. The results indicate that the lowest RMSE for out-of-sample forecasts of cattle prices is obtained using a gradually switching VAR model. However, differences between the gradually switching VAR model and a univariate ARIMA model are not strongly significant. Impulse response functions indicate that adjustments of cattle prices to new information have become faster in recent years.

scholarly journals Sequence and functional characterization of hypoxia-inducible factors, HIF1α, HIF2αa, and HIF3α, from the estuarine fish, Fundulus heteroclitus

2017 ◽  
Vol 312 (3) ◽  
pp. R412-R425 ◽  
Author(s):  
Ian K. Townley ◽  
Sibel I. Karchner ◽  
Elena Skripnikova ◽  
Thomas E. Wiese ◽  
Mark E. Hahn ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Fundulus Heteroclitus ◽  
Phylogenetic Analyses ◽  
Functional Characterization ◽  
Hypoxia Inducible Factor ◽  
Estuarine Fish ◽  
Low Oxygen ◽  
Aryl Hydrocarbon ◽  
Transactivation Domains

The hypoxia-inducible factor (HIF) family of transcription factors plays central roles in the development, physiology, pathology, and environmental adaptation of animals. Because many aquatic habitats are characterized by episodes of low dissolved oxygen, fish represent ideal models to study the roles of HIF in the response to aquatic hypoxia. The estuarine fish Fundulus heteroclitus is found in habitats prone to hypoxia. It responds to low oxygen via behavioral, physiological, and molecular changes, and one member of the HIF family, HIF2α, has been previously described. Herein, cDNA sequencing, phylogenetic analyses, and genomic approaches were used to determine other members of the HIFα family from F. heteroclitus and their relationships to HIFα subunits from other vertebrates. In vitro and cellular approaches demonstrated that full-length forms of HIF1α, HIF2α, and HIF3α independently formed complexes with the β-subunit, aryl hydrocarbon receptor nuclear translocator, to bind to hypoxia response elements and activate reporter gene expression. Quantitative PCR showed that HIFα mRNA abundance varied among organs of normoxic fish in an isoform-specific fashion. Analysis of the F. heteroclitus genome revealed a locus encoding a second HIF2α—HIF2αb—a predicted protein lacking oxygen sensing and transactivation domains. Finally, sequence analyses demonstrated polymorphism in the coding sequence of each F. heteroclitus HIFα subunit, suggesting that genetic variation in these transcription factors may play a role in the variation in hypoxia responses among individuals or populations.

scholarly journals Genome wide identification and predicted functional analyses of NAC transcription factors in Asian pears

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Mudassar Ahmad ◽  
Xinhui Yan ◽  
Jianzhao Li ◽  
Qinsong Yang ◽  
Wajeeha Jamil ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Nac Transcription Factors ◽  
Genome Wide ◽  
Functional Analyses

scholarly journals Inducing the attachment of cable bacteria on oxidizing electrodes

2020 ◽  
Vol 17 (3) ◽  
pp. 597-607 ◽  
Author(s):  
Cheng Li ◽  
Clare E. Reimers ◽  
Yvan Alleau
Keyword(s):  
Phylogenetic Analyses ◽  
Sulfide Oxidation ◽  
Lower Number ◽  
Filamentous Bacteria ◽  
Mineral Precipitation ◽  
Electrode Surfaces ◽  
New Information ◽  
The Family ◽  
Electron Donation

Abstract. Cable bacteria (CB) are multicellular, filamentous bacteria within the family of Desulfobulbaceae that transfer electrons longitudinally from cell to cell to couple sulfide oxidation and oxygen reduction in surficial aquatic sediments. In the present study, electrochemical reactors that contain natural sediments are introduced as a tool for investigating the growth of CB on electrodes poised at an oxidizing potential. Our experiments utilized sediments from Yaquina Bay, Oregon, USA, and we include new phylogenetic analyses of separated filaments to confirm that CB from this marine location cluster with the genus “Candidatus Electrothrix”. These CB may belong to a distinctive lineage, however, because their filaments contain smaller cells and a lower number of longitudinal ridges compared to cables described from other locales. The results of a 135 d bioelectrochemical reactor experiment confirmed that these CB can migrate out of reducing sediments and grow on oxidatively poised electrodes suspended in anaerobic seawater. CB filaments and several other morphologies of Desulfobulbaceae cells were observed by scanning electron microscopy and fluorescence in situ hybridization on electrode surfaces, albeit in low densities and often obscured by mineral precipitation. These findings provide new information to suggest what kinds of conditions will induce CB to perform electron donation to an electrode surface, further informing future experiments to culture CB outside of a sediment matrix.

Small-subunit rRNA gene sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 1. Evidence for the Plocamiales ord.nov.

1994 ◽  
Vol 72 (9) ◽  
pp. 1250-1263 ◽  
Author(s):  
G. W. Saunders ◽  
G. T. Kraft
Keyword(s):  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Chain Reaction ◽  
Small Subunit Rrna Gene ◽  
New Information ◽  
The Family ◽  
Close Relationship ◽  
Polymerase Chain

Nucleotide sequences of the nuclear, small-subunit (SSU) ribosomal RNAs, as inferred from polymerase chain reaction (PCR)-amplified products, are presented for Areschougia congesta (Turner) J. Agardh (Solieriaceae), Dasyphloea insignis Montagne (Dumontiaceae), Sarcothalia crassifolia (C. Agardh) Edyvane & Womersley (Gigartinaceae), Nizymenia australis Sonder (Nizymeniaceae), Phacelocarpus peperocarpos (Poiret) Wynne, Ardré & Silva (Phacelocarpaceae), Plocamiocolax pulvinata Setchell, Plocamium angustum (J. Agardh) J.D. Hooker, Plocamium cartilagineum (Linnaeus) Dixon (Plocamiaceae), Rhodymenia linearis J. Agardh (Rhodymeniaceae), and Sphaerococcus coronopifolius Stackhouse (Sphaerococcaceae). Phylogenetic analyses of the SSU sequences between the Plocamiaceae and members of the Sphaerococcaceae, Phacelocarpaceae, and Nizymeniaceae, with which the Plocamiaceae has been associated historically, show SSU differences of between 87 and 105 nucleotides and do not indicate a close relationship. A review of anatomical knowledge of the Plocamiaceae and Pseudoanemoniaceae and new information on vegetative and tetrasporangial development in Plocamium and Plocamiocolax are presented to buttress a case for the Plocamiales ord.nov. Representatives of the Nizymeniaceae and Phacelocarpaceae differ from one another by only nine nucleotides, suggesting that these two taxa are very closely related and perhaps not distinct at the family rank. Key words: Gigartinales, PCR, phylogeny, Plocamiales ord.nov., Pseudoanemoniaceae, Rhodophyta, small-subunit rRNA, systematics.

scholarly journals Molecular Evidence of Bartonella melophagi in Ticks in Border Areas of Xinjiang, China

2021 ◽  
Vol 8 ◽  
Author(s):  
Jun Ni ◽  
Qiaoyun Ren ◽  
Hanliang Lin ◽  
Malike Aizezi ◽  
Jin Luo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analyses ◽  
Domestic Animals ◽  
Molecular Evidence ◽  
Intracellular Bacteria ◽  
Land Area ◽  
Pcr Assay ◽  
New Information ◽  
Border Areas ◽  
Pcr Assays

Bartonella are gram-negative intracellular bacteria; certain species of Bartonella can cause diseases in mammals and humans. Ticks play a major role in the transmission of Bartonella. Xinjiang is the largest province in China according to land area and has one-third of the tick species in China; the infection rate of Bartonella in ticks in the Xinjiang border areas has not been studied in detail. Therefore, this study investigated tick infections by Bartonella in Xinjiang border areas, and the purpose of the study was to fill in gaps in information regarding the genetic diversity of tick infections by Bartonella in Xinjiang. We tested 1,549 tick samples from domestic animals (sheep and cattle) for Bartonella using ribC-PCR. Positive samples from the ribC-PCR assay for Bartonella spp. were further subjected to PCR assays targeting the ITS, rpoB and gltA genes followed by phylogenetic analyses. Bartonella DNA was detected in 2.19% (34/1,549) of tick samples, and the ITS, rpoB and gltA genes of ribC gene-positive samples were amplified to identify nine samples of Bartonella melophagi. In this study, molecular analysis was used to assess the presence and genetic diversity of B. melophagi in ticks collected from sheep and cattle from Xinjiang, China. This study provides new information on the presence and identity of B. melophagi in ticks from sheep and cattle.

Paedomorphosis, Aristotle's lantern, and the origin of the sand dollars (Echinodermata: Clypeasteroida)

Paleobiology ◽  
1990 ◽  
Vol 16 (1) ◽  
pp. 25-48 ◽  
Author(s):  
Rich Mooi
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
New Classification ◽  
Crown Group ◽  
New Information ◽  
Sand Dollars ◽  
Fossil Genus ◽  
Tube Feet

Convincing hypotheses of the origin of major invertebrate groups are difficult to make in the absence of phylogenetic analyses. In spite of this, several scenarios exist for the origin of the unusual echinoid order Clypeasteroida. I expand upon the most probable of these models by performing a phylogenetic analysis on three clypeasteroid suborders, the enigmatic fossil genusTogocyamus, and the extinct Oligopygoida. This analysis shows that the oligopygoids are the sister group of the Clypeasteroida plusTogocyamus. The latter is here considered a plesion (extinct sister group) to the crown group Clypeasteroida. Within that order, the suborder Clypeasterina is the sister group to the Laganina plus Scutellina. A new classification of all these taxa is presented. The phylogeny is based on 47 characters and incorporates data on external appendages, Aristotle's lantern anatomy, and test structure of irregular echinoids, as well as new information on the morphology ofTogocyamus. The earliest clypeasteroids had a lantern similar to that of adult oligopygoids, which in turn inherited their lantern from a cassiduloid-like ancestor that retained the lantern into adulthood. This lantern is absent in adult cassiduloids. Subsequent changes, including modification of the lantern into a crushing mill, extreme flattening of the test, and proliferation of food-gathering tube feet have allowed clypeasteroids to become epifaunal inhabitants of environments characterized by fine, shifting substrates, a habitat previously inaccessible to most other irregular echinoids.

scholarly journals Jenynsia luxata, a new species from Northwestern Argentina, with additional observations of J. maculataRegan and phylogeny of the genus (Cyprinodontiformes: Anablepidae)

2013 ◽  
Vol 11 (3) ◽  
pp. 565-572 ◽  
Author(s):  
Gastón Aguilera ◽  
Juan Marcos Mirande ◽  
Pablo A. Calviño ◽  
Luis Fernando Lobo
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Northwestern Argentina ◽  
Pelvic Bones ◽  
New Information ◽  
Left And Right ◽  
Equal Weighting ◽  
A New Species

Jenynsia luxata, a new species from northwestern Argentina, is described. This species is diagnosable from all other Jenynsia by the medial processes of left and right pelvic bones relatively reduced and separated from each other. The new species resembles J. multidentata, but it is further distinguished from this species by the absence of a swelling between the urogenital opening and the anterior base of the anal fin in females and details of coloration. Phylogenetic analyses, both under implied and equal weighting, recover the subgenera Plesiojenynsia and Jenynsia as monophyletic units. New information on previously missing characters of Jenynsia maculata is added. These data and phylogenetic characters coded for the new species herein described contribute to a better resolution of the phylogenetic relationships within the subgenus Jenynsia, which is herein supported by additional synapomorphies relative to previous phylogenies.

scholarly journals Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix)

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 243 ◽  
Author(s):  
Alexandru Tomazatos ◽  
Rachel E. Marschang ◽  
Iulia Maranda ◽  
Heike Baum ◽  
Alexandra Bialonski ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Sand Fly ◽  
Intragenic Recombination ◽  
Surveillance Program ◽  
Biting Midges ◽  
Natrix Natrix ◽  
New Information ◽  
Gene Reassortment ◽  
Virus Strains

The discovery and characterization of novel arthropod-borne viruses provide valuable information on their genetic diversity, ecology, evolution and potential to threaten animal or public health. Arbovirus surveillance is not conducted regularly in Romania, being particularly very scarce in the remote and diverse areas like the Danube Delta. Here we describe the detection and genetic characterization of a novel orbivirus (Reoviridae: Orbivirus) designated as Letea virus, which was found in grass snakes (Natrix natrix) during a metagenomic and metatranscriptomic survey conducted between 2014 and 2017. This virus is the first orbivirus discovered in reptiles. Phylogenetic analyses placed Letea virus as a highly divergent species in the Culicoides-/sand fly-borne orbivirus clade. Gene reassortment and intragenic recombination were detected in the majority of the nine Letea virus strains obtained, implying that these mechanisms play important roles in the evolution and diversification of the virus. However, the screening of arthropods, including Culicoides biting midges collected within the same surveillance program, tested negative for Letea virus infection and could not confirm the arthropod vector of the virus. The study provided complete genome sequences for nine Letea virus strains and new information about orbivirus diversity, host range, ecology and evolution. The phylogenetic associations warrant further screening of arthropods, as well as sustained surveillance efforts for elucidation of Letea virus natural cycle and possible implications for animal and human health.

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