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1. 139 sex-specific gene expression in porcine pre-implantation embryos

Author:
D. Kradolfer; J. Knubben; V. Flöter; J. Bick; S. Bauersachs; S. E. Ulbrich
Source:
Reproduction, fertility, and development 2016 v.28 no.2 pp. 199
ISSN:
1031-3613
Subject:
DNA; German Landrace; National Center for Biotechnology Information; Pietrain; X chromosome; autosomes; blastocyst; boars; embryogenesis; gene expression; genes; genome assembly; in vitro fertilization; messenger RNA; microRNA; nitrogen; ovulation; pH; sows; spermatozoa; statistical analysis; transcription (genetics); uterus; California
Abstract:
... X-Chromosome inactivation in female mammals starts during early blastocyst stage with expression of the X-inactive specific transcript (XIST), which coats and silences the inactive X chromosome. However, this compensation is not complete in blastocysts, as a large number of X-linked transcripts are more highly expressed in female embryos than in males. Furthermore, the process of X chromosome inac ...
DOI:
10.1071/RDv28n2Ab138

2. 14 epigenetic changes in equine spermatozoa during cryopreservation: a preliminary study

Author:
C. Aurich; B. Schreiner; N. Ille; M. Alvarenga; D. Scarlet
Source:
Reproduction, fertility, and development 2016 v.28 no.2 pp. 136-137
ISSN:
1031-3613
Subject:
DNA; DNA methylation; Shetland Pony; breeding; computer software; conception; cooling; cryopreservation; cryoprotectants; cytosine; denaturation; enzyme-linked immunosorbent assay; epigenetics; freeze-thaw cycles; freezing; glycerol; insemination; mares; monoclonal antibodies; semen; spermatozoa; stallions; statistical analysis; California; Sweden
Abstract:
... The use of cryopreserved semen for insemination of mares facilitates breeding management but often results in reduced conception rates. This has been mainly attributed to changes in sperm membrane function caused by the freezing-thawing procedure. However, semen processing may also contribute to epigenetic changes in spermatozoa. In the present study, we therefore addressed changes in sperm DNA-me ...
DOI:
10.1071/RDv28n2Ab13

3. Abalone Withering Syndrome Disease Dynamics: Infectious Dose and Temporal Stability in Seawater

Author:
Lisa M. Crosson; Nina S. Lottsfeldt; Mariah E. Weavil‐Abueg; Carolyn S. Friedman
Source:
Journal of aquatic animal health 2020 v.32 no.2 pp. 83-92
ISSN:
0899-7659
Subject:
DNA; Haliotis rufescens; abalone; animal health; aquatic animals; bacteria; farms; feces; histology; juveniles; pathogens; protocols; quantitative polymerase chain reaction; risk; seawater; temperature; California
Abstract:
... Withering syndrome (WS) is a chronic bacterial disease that affects numerous northeastern Pacific abalone Haliotis spp. The causative agent of WS is an obligate intracellular Rickettsiales‐like bacterium (WS‐RLO) that remains unculturable, thereby limiting our understanding of WS disease dynamics. The objectives of our study were to (1) determine the temporal stability of WS‐RLO DNA outside of its ...
DOI:
10.1002/aah.10102

4. Abiotic and Biotic Contributors to Support Inter-Epidemic Francisella tularensis in an Agricultural Peri-Urban Environment

Author:
Roth Tara M.; Foley Janet; Wright Stan
Source:
Vector borne and zoonotic diseases 2017 v.17 no.11 pp. 764-772
ISSN:
1557-7759
Subject:
Culicidae; DNA; Didelphis virginiana; Francisella tularensis; Rattus rattus; Sciuridae; Siphonaptera; aquatic invertebrates; carnivores; cats; enzootic diseases; enzyme-linked immunosorbent assay; feral animals; habitats; hematophagous insects; opossums; quantitative polymerase chain reaction; rodents; seroprevalence; ticks; tularemia; California
Abstract:
... To characterize the inter-epidemic ecology of Francisella tularensis, we surveyed vertebrates and invertebrates for the abundance, spatial distribution, and status of infection at a site in northern California that had evidence of endemic type B tularemia. We collected 2910 mosquitoes, 77 biting flies, 704 ticks, 115 mammals, and 1911 aquatic invertebrates in 2013–2014. Real-time PCR on all mosqui ...
DOI:
10.1089/vbz.2017.2148

5. Activating mutations in the catalytic or juxtamembrane domain of c-kit in splenic mast cell tumors of cats

Author:
Dank, Gillian; Chien, May B.; London, Cheryl A.
Source:
American journal of veterinary research 2002 v.63 no.8 pp. 1129-1133
ISSN:
0002-9645
Subject:
DNA; active sites; agarose; cats; databases; dogs; exons; gel electrophoresis; humans; medical education; mutation; neoplasms; polymerase chain reaction; proto-oncogenes; therapeutics; California
Abstract:
... Objective-To evaluate splenic mast cell tumors (MCT) of cats for activating mutations in the protooncogene c-kit. Sample Population-10 formalin-fixed, paraffinembedded splenic MCT from cats in the pathology database of the Veterinary Medical Teaching Hospital at the University of California, Davis. Procedure-Genomic DNA was isolated from tumor specimens, and the polymerase chain reaction (PCR) pro ...
DOI:
10.2460/ajvr.2002.63.1129

6. Adaptation of a Phytophthora ramorum Real-Time Polymerase Chain Reaction Assay Based on a Mitochondrial Gene Region for Use on the Cepheid SmartCycler

Author:
K. E. Sechler; M. M. Carras; N. Shishkoff; P. W. Tooley
Source:
Plant health progress 2010 v.11 no.1 pp. -
ISSN:
1535-1025
Subject:
DNA; Phytophthora kernoviae; Phytophthora ramorum; cross reaction; detection limit; freeze drying; mitochondria; mitochondrial genes; quantitative polymerase chain reaction; quarantine; reverse transcriptase polymerase chain reaction; California
Abstract:
... Detection of Phytophthora ramorum in US commercial nurseries has led to a number of quarantine regulations. Methods such as real-time PCR (RT-PCR) provide rapid and reliable detection that can supplement attempts to culture P. ramorum from symptomatic tissue. We adapted and optimized a previously described mitochondrial gene-based RT-PCR assay for use with a Cepheid SmartCycler v.1 and ready-to-us ...
DOI:
10.1094/PHP-2010-0212-01-RS

7. Amanita vernicoccora sp. nov.--the vernal fruiting 'coccora' from California

Author:
Bojantchev, Dimitar; Pennycook, Shaun R.; Davis, R. Michael
Source:
Mycotaxon 2011 v.117 pp. 485-497
ISSN:
0093-4666
Subject:
Amanita; DNA; fruiting; new species; phenotype; sequence analysis; California
Abstract:
... We describe Amanita vernicoccora, a vernal fruiting species known as the "spring coccora" in California. Sequence analyses of four DNA regions and phenotypic traits demonstrate that A. vernicoccora, long considered a pale-colored form of the autumnal fruiting A. calyptroderma (the 'fall coccora'), is a unique species. Morphological and genetic data support both species in section Caesareae. We als ...
DOI:
10.5248/117.485

8. Analyses of the Population Structure in a Global Collection of Phytophthora nicotianae Isolates Inferred from Mitochondrial and Nuclear DNA Sequences

Author:
Mammella Marco A.; Martin Frank N.; Cacciola Santa O.; Coffey Michael D.; Faedda Roberto; Schena Leonardo
Source:
Phytopathology 2013 v.103 no.6 pp. 610-622
ISSN:
0031-949X
Subject:
Citrus; DNA; Nicotiana; Phytophthora nicotianae; Solanum; alleles; genetic recombination; genetic variation; haplotypes; heterozygosity; hosts; loci; mitochondria; nuclear genome; nucleotide sequences; plant pathogens; population growth; population structure; single nucleotide polymorphism; Albania; California; Florida; Italy; Philippines; Syria
Abstract:
... Genetic variation within the heterothallic cosmopolitan plant pathogen Phytophthora nicotianae was determined in 96 isolates from a wide range of hosts and geographic locations by characterizing four mitochondrial (10% of the genome) and three nuclear loci. In all, 52 single-nucleotide polymorphisms (SNPs) (an average of 1 every 58 bp) and 313 sites with gaps representing 5,450 bases enabled the i ...
DOI:
10.1094/PHYTO-10-12-0263-R

9. Ancient DNA evidence for the regional trade of bear paws by Chinese diaspora communities in 19th-century western North America

Author:
J. Ryan Kennedy; Leland Rogers; Frederika A. Kaestle
Source:
Journal of archaeological science 2018 v.99 pp. 135-142
ISSN:
0305-4403
Subject:
Chinese people; DNA; Ursus arctos; animal products; archaeology; food availability; genetic markers; markets; models; trade; wild animals; Alberta; British Columbia; California
Abstract:
... This study presents the results of ancient DNA (aDNA) analysis of a bear paw bone recovered from the Market Street Chinatown, a 19ᵗʰ-century Chinese community in San José, California. This analysis reveals that this bone derived from a Brown Bear (Ursus arctos) sharing genetic markers found only in Brown Bear populations living in southwestern Alberta and southeastern British Columbia, Canada. The ...
DOI:
10.1016/j.jas.2018.09.005

10. Antibiotic Resistance in Airborne Bacteria Near Conventional and Organic Beef Cattle Farms in California, USA

Author:
Helen M. Sancheza; Cristina Echeverria; Vanessa Thulsiraj; Amy Zimmer-Faust; Ariel Flores; Madeleine Laitz; Gregory Healy; Shaily Mahendra; Suzanne E. Paulson; Yifang Zhu; Jennifer A. Jay
Source:
Water, air, and soil pollution 2016 v.227 no.8 pp. 280
ISSN:
0049-6979
Subject:
DNA; air; airborne microorganisms; antibiotic resistance; bacteria; beef cattle; cefoperazone; cloxacillin; farms; filters; genes; monitoring; organic foods; quantitative polymerase chain reaction; rearing; California
Abstract:
... Levels of antibiotic resistance genes (ARGs) and the fractions of antibiotic resistant bacteria (ARB) among culturable heterotrophic bacteria were compared in outdoor air near conventional (n = 3) and organic (n = 3) cattle rearing facilities. DNA extracts from filters taken from 18 locations were analyzed by quantitative polymerase chain reaction (qPCR) for five ARGs. At the reference (non-agricu ...
DOI:
10.1007/s11270-016-2979-8

11. Application of Phylogenetic Microarray Analysis to Discriminate Sources of Fecal Pollution

Author:
Dubinsky Eric A.; Esmaili Laleh; Hulls John R.; Cao Yiping; Griffith John F.; Andersen Gary L.
Source:
Environmental Science & Technology 2012 v.46 no.8 pp. 4340-4347
ISSN:
1520-5851
Subject:
ribosomal RNA; grazing; cluster analysis; phylogeny; Clostridia; genes; cows; biomarkers; DNA; feces; pollution; bacterial communities; Actinobacteria; sequence analysis; community structure; Bacilli; humans; DNA microarrays; gamma-Proteobacteria; birds; Bacteroidetes; elks; microbial contamination; nucleotide sequences; horses; bacteria; California
Abstract:
... Conventional methods for fecal source tracking typically use single biomarkers to systematically identify or exclude sources. High-throughput DNA sequence analysis can potentially identify all sources of microbial contaminants in a single test by measuring the total diversity of fecal microbial communities. In this study, we used phylogenetic microarray analysis to determine the comprehensive suit ...
DOI:
10.1021/es2040366

12. Application of ddPCR for detection of Enterococcus spp. in coastal water quality monitoring

Author:
Chad Crain; Keith Kezer; Syreeta Steele; Judith Owiti; Sphoorthy Rao; Maria Victorio; Brett Austin; Alon Volner; William Draper; John Griffith; Joshua Steele; Marva Seifert
Source:
Journal of microbiological methods 2021 v.184 pp. 106206
ISSN:
0167-7012
Subject:
DNA; Enterococcus; coastal water; data collection; droplets; equations; gene dosage; most probable number technique; pollution; water quality; California
Abstract:
... Droplet digital polymerase chain reaction (ddPCR) was evaluated for the detection of fecal indicator bacteria (FIB), Enterococcus spp., in San Diego County beach water samples collected under diverse conditions, from multiple pollution sources, as part of regulatory monitoring activities over 20 months. Two US EPA-approved methods, qPCR (EPA 1609.1) and Enterolert (SM9230D), were used as reference ...
DOI:
10.1016/j.mimet.2021.106206

13. Arbuscular mycorrhizal colonization of giant sequoia (Sequoiadendron giganteum) in response to restoration practices

Author:
Catherine Fahey; Robert A. York; Teresa E. Pawlowska
Source:
Mycologia 2012 v.104 no.5 pp. 988-997
ISSN:
1557-2536
Subject:
DNA; Glomus; Sequoiadendron giganteum; carbon; carbon dioxide fixation; forest canopy; genotyping; mineral soils; mountains; natural regeneration; sapling growth; vesicular arbuscular mycorrhizae; California
Abstract:
... Interactions with soil microbiota determine the success of restoring plants to their native habitats. The goal of our study was to understand the effects of restoration practices on interactions of giant sequoia Sequoiadendron giganteum with arbuscular mycorrhizal (AM) fungi (Glomeromycota). Natural regeneration of Sequoiadendron is threatened by the absence of severe fires that create forest cano ...
DOI:
10.3852/11-289

14. Assessment of the order Rhodymeniales (Rhodophyta) from British Columbia using an integrative taxonomic approach reveals overlooked and cryptic species diversity

Author:
Gina V. Filloramo; Gary W. Saunders
Source:
Botany 2018 v.96 no.6 pp. 359-383
ISSN:
1916-2804
Subject:
Botryocladia; DNA; Fryeella; cryptic species; genetic analysis; new combination; new species; nucleotide sequences; species diversity; uncertainty; British Columbia; California
Abstract:
... Molecular-assisted alpha taxonomy using COI-5P and rbcL-3P was employed to reassess species diversity for the Rhodymeniales (Rhodophyta) in British Columbia. A total of 563 collections from British Columbia were resolved as 16 genetic species groups, whereas 13 were previously reported. Collections attributed to Botryocladia pseudodichotoma from British Columbia were resolved as distinct from coll ...
DOI:
10.1139/cjb-2017-0143

15. Association of the pitch canker pathogen Fusarium circinatum with grass hosts in commercial pine production areas of South Africa

Author:
Cassandra L Swett; Bernice Porter; Gerda Fourie; Emma T Steenkamp; Thomas R Gordon; Michael J Wingfield
Source:
Southern forests 2014 v.76 no.3 pp. 161-166
ISSN:
2070-2639
Subject:
Briza maxima; DNA; Ehrharta; Fusarium circinatum; Pinus; Pseudotsuga menziesii; disease occurrence; endophytes; forests; fungi; grasses; host range; hosts; inoculum; nucleotide sequences; pathogens; plantations; sanitation; virulence; California; South Africa
Abstract:
... The pitch canker pathogen, Fusarium circinatum , has major impacts on production in pine nurseries and plantations in South Africa. Thus far, efforts to reduce local spread have focused on rouging of infected pines and sanitation to eliminate local sources of inoculum. Although the host range of F. circinatum was thought to be limited to pines and Douglas-fir, recent studies in California indicate ...
DOI:
10.2989/20702620.2014.916087

16. Atypical chlamydiaceae in wild populations of hawks (buteo spp.) in california

Author:
Charlene Luján-Vega; Michelle G. Hawkins; Christine K. Johnson; Christopher Briggs; Chris Vennum; Peter H. Bloom; Joshua M. Hull; Carolyn Cray; Denise Pesti; Lisa Johnson; Paula Ciembor; Branson R. Ritchie
Source:
Journal of zoo and wildlife medicine 2018 v.49 no.1 pp. 108-115
ISSN:
1937-2825
Subject:
Buteo jamaicensis; Buteo swainsoni; Chlamydia; DNA; DNA fragmentation; Ondatra zibethicus; agglutination tests; antibodies; birds of prey; cross reaction; epidemiology; fledglings; fluorescent antibody technique; genes; genotype; hares; hawks; hosts; immunoglobulin Y; juveniles; melting; nucleotide sequences; quantitative polymerase chain reaction; sequence analysis; serology; California
Abstract:
... Chlamydiaceae bacteria infect many vertebrate hosts, and previous reports based on polymerase chain reaction (PCR) assays and serologic assays that are prone to cross-reaction among chlamydial organisms have been used to describe the prevalence of either DNA fragments or antibodies to Chlamydia spp. in wild raptorial populations. This study reports the PCR-based prevalence of Chlamydiaceae DNA tha ...
DOI:
10.1638/2017-0053R.1

17. Avian Mycobacteriosis in Psittacines: A Retrospective Study of 123 Cases

Author:
C. Palmieri; P. Roy; A.S. Dhillon; H.L. Shivaprasad
Source:
Journal of comparative pathology 2013 v.148 no.2-3 pp. 126-138
ISSN:
0021-9975
Subject:
DNA; Mycobacterium avium; Mycobacterium genavense; animal health; bacteria; biosafety; food safety; genes; giant cells; heat shock proteins; histopathology; macrophages; mixed infection; mucosa; necropsy; parakeets; parrots; polymerase chain reaction; restriction mapping; retrospective studies; spleen; California
Abstract:
... One hundred and twenty-three cases of mycobacterioses were diagnosed in psittacine birds from a total of 9,241 submissions for necropsy examination or histopathology made to the California Animal Health and Food Safety Laboratory System between 1990 and 2007. The species affected most commonly were Amazon parrots (Amazona spp.)(n = 32; 26%) and grey-cheeked parakeets Brotogeris pyrrophterus (n = 2 ...
DOI:
10.1016/j.jcpa.2012.06.005
PubMed:
22884283

18. Beet curly top virus Strains Associated with Sugar Beet in Idaho, Oregon, and a Western U.S. Collection

Author:
Strausbaugh Carl A.; Eujayl Imad A.; Wintermantel William M.
Source:
Plant disease 2017 v.101 no.8 pp. 1373-1382
ISSN:
0191-2917
Subject:
Beet curly top virus; Circulifer tenellus; DNA; disease severity; leaves; mixed infection; polymerase chain reaction; sequence analysis; sugar beet; California; Colorado; Idaho; Oregon
Abstract:
... Curly top of sugar beet is a serious, yield-limiting disease in semiarid production areas caused by Beet curly top virus (BCTV) and transmitted by the beet leafhopper. One of the primary means of control for BCTV in sugar beet is host resistance but effectiveness of resistance can vary among BCTV strains. Strain prevalence among BCTV populations was last investigated in Idaho and Oregon during a 2 ...
Handle:
10113/5722679
DOI:
10.1094/PDIS-03-17-0381-RE

19. California walnut improvement program: scion breeding and rootstock development

Author:
C. A. Leslie; G. H. McGranahan
Source:
Acta horticulturae 2013 no.1050 pp. 81-88
ISSN:
0567-7572
Subject:
Cherry leaf roll virus; DNA; Juglans hindsii; Juglans regia; Nematoda; Phytophthora; bioinformatics; breeding; color; crown galls; cultivars; farms; genetic resistance; genomics; genotype; growers; harvest date; hybrids; industry; micropropagation; pathogens; phenotype; planting; rootstocks; scions; seeds; university programs; walnuts; California
Abstract:
... The goals of the University of California-Davis Walnut Improvement Program are to develop improved scion and rootstock cultivars for the California walnut industry and to utilize emerging genomic tools to increase breeding efficiency. Scion breeding objectives include new cultivars with early harvest dates, light kernel color, and resistance to blight and the development of scions with resistance ...

20. Cerebral Angiostrongylus cantonensis infection in a captive African pygmy falcon (Polihierax semitorquatus) in southern California

Author:
Rachel E. Burns; Elizabeth J. Bicknese; Yvonne Qvarnstrom; Marlene DeLeon-Carnes; Clifton P. Drew; Chris H. Gardiner; Bruce A. Rideout
Source:
Journal of veterinary diagnostic investigation v.26 no.5 pp. 695-698
ISSN:
1943-4936
Subject:
DNA; Hemidactylus; Parastrongylus cantonensis; brain; falcons; females; histology; lungworms; meningoencephalitis; polymerase chain reaction; rats; zoos; California; South East Asia
Abstract:
... A 10-month-old, female African pygmy falcon (Polihierax semitorquatus) hatched and housed at the San Diego Zoo developed neurologic signs and died from a cerebral infection with the rat lungworm Angiostrongylus cantonensis. There was an associated mild nonsuppurative meningoencephalitis. This infection was diagnosed on histology and confirmed by detection of species-specific A. cantonensis DNA in ...
DOI:
10.1177/1040638714544499