bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐wide SNP analysis reveals a genetic basis for sea‐age variation in a wild population of Atlantic salmon (Salmo salar)
Authors: Johnston Susan E. , Orell Panu , Pritchard Victoria L. , Kent Matthew P. , Lien Sigbjørn , Niemelä Eero , Erkinaro Jaakko , Primmer Craig R. 
Published: June 2014

AbstractDelaying sexual maturation can lead to larger body size and higher reproductive success, but carries an increased risk of death before reproducing. Classical life history theory predicts that trade‐offs between reproductive success and survival should lead to the evolution of an optimal strategy in a given population. However, variation in mating strategies generally persists, and in general, there remains a poor understanding of genetic and physiological mechanisms underlying this variation. One extreme case of this is in the Atlantic salmon (Salmo salar), which can show variation in the age at which they return from their marine migration to spawn (i.e. their ‘sea age’). This results in large size differences between strategies, with direct implications for individual fitness. Here, we used an Illumina Infinium SNP array to identify regions of the genome associated with variation in sea age in a large population of Atlantic salmon in Northern Europe, implementing individual‐based genome‐wide association studies (GWAS) and population‐based FST outlier analyses. We identified several regions of the genome which vary in association with phenotype and/or selection between sea ages, with nearby genes having functions related to muscle development, metabolism, immune response and mate choice. In addition, we found that individuals of different sea ages belong to different, yet sympatric populations in this system, indicating that reproductive isolation may be driven by divergence between stable strategies. Overall, this study demonstrates how genome‐wide methodologies can be integrated with samples collected from wild, structured populations to understand their ecology and evolution in a natural context.
Diversity among Pseudomonas corrugata and Pseudomonas mediterranea isolated from tomato and pepper showing symptoms of pith necrosis in Greece
Authors: Trantas E. A. , Sarris P. F. , Pentari M. G. , Mpalantinaki E. E. , Ververidis F. N. , Goumas D. E. 
Published: June 2014

Bacterial isolates from tomato plants with symptoms revealing pith necrosis collected over a 20‐year period were screened and characterized using biochemical and pathogenicity tests, as well as molecular approaches. The examined isolates were categorized into two main Pseudomonas species: P. corrugata and P. mediterranea. The diversity of these isolates was characterized through a variety of biochemical, serological, pathogenicity, DNA fingerprinting and multi‐locus sequence analysis features. Of the total Pseudomonas isolates causing pith necrosis, the biochemical profile of the selected non‐fluorescent pseudomonads consisting of P. corrugata and P. mediterranea revealed differentiation in only three characters among 43 examined. Serological analysis managed to identify the P. corrugata isolates using the laboratory prepared antiserum anti‐PC14. Genomic analyses using rep‐PCR fingerprinting and multilocus sequence analysis (MLSA) revealed considerable inter‐ and intraspecies genetic diversity. However, artificial inoculations of several plant species revealed similar pathogenicity patterns for both P. corrugata and P. mediterranea isolates. These results provide the basis for a more comprehensive understanding of the biology, sources and shift in genetic diversity and evolution of both P. corrugata and P. mediterranea populations and could support the development of molecular identification tools and epidemiological studies in diseases caused by these species. Moreover, this is the first report of P. mediterranea in Greece on tomato as well as on pepper plants.
Hybridization between Japanese and North American Chlamydomonas reinhardtii (Volvocales, Chlorophyceae)
Authors: Nakada Takashi , Tsuchida Yudai , Arakawa Kazuharu , Ito Takuro , Tomita Masaru 
Published: June 2014

SummaryThe microalga Chlamydomonas reinhardtii is a model organism whose whole genome has been sequenced. Although considered a cosmopolitan species, only eastern North American isolates of C. reinhardtii were available before 2010, when new Japanese isolates were reported. In the study describing the new Japanese isolates, zygote formation between Japanese and North American strains was shown, but germination was not demonstrated. In this study, the germination of intercontinental hybrid zygotes was examined using wild‐type Japanese strains and mutant American strains that cannot utilize nitrate. Several clonal progeny strains were established, and the progeny strains were screened based on mating type and nitrate utilization to confirm their hybrid nature. The establishment of four intercontinental hybrid strains with different phenotypic combinations was confirmed by sequencing mating type‐specific and nitrate reductase‐related genes. The potential for hybrid formation between Japanese and North American strains suggests the existence of a worldwide mating population of C. reinhardtii.
Energized by love: Thinking about romantic relationships increases positive affect and blood glucose levels
Authors: Stanton Sarah C. E. , Campbell Lorne , Loving Timothy J. 
Published: June 2014

AbstractWe assessed the impact of thinking of a current romantic partner on acute blood glucose responses and positive affect over a short period of time. Participants in romantic relationships were randomly assigned to reflect on their partner, an opposite‐sex friend, or their morning routine. Blood glucose levels were assessed prior to reflection, as well as at 10 and 25 min postreflection. Results revealed that individuals in the routine and friend conditions exhibited a decline in glucose over time, whereas individuals in the partner condition did not exhibit this decline (rather, a slight increase) in glucose over time. Reported positive affect following reflection was positively associated with increases in glucose, but only for individuals who reflected on their partner, suggesting this physiological response reflects eustress. These findings add to the literature on eustress in relationships and have implications for relationship processes.
Caspase Activation, Hydrogen Peroxide Production and Akt Dephosphorylation Occur During Stallion Sperm Senescence
Authors: Gallardo Bolaños JM , Balao da Silva C , Martín Muñoz P , Plaza Dávila M , Ezquerra J , Aparicio IM , Tapia JA , Ortega Ferrusola C , Peña FJ 
Published: June 2014

ContentsTo investigate the mechanisms inducing sperm death after ejaculation, stallion ejaculates were incubated in BWW media during 6 h at 37°C. At the beginning of the incubation period and after 1, 2, 4 and 6 h sperm motility and kinematics (CASA), mitochondrial membrane potential and membrane permeability and integrity were evaluated (flow cytometry). Also, at the same time intervals, active caspase 3, hydrogen peroxide, superoxide anion (flow cytometry) and Akt phosphorylation (flow cytometry) were evaluated. Major decreases in sperm function occurred after 6 h of incubation, although after 1 h decrease in the percentages of motile and progressive motile sperm occurred. The decrease observed in sperm functionality after 6 h of incubation was accompanied by a significant increase in the production of hydrogen peroxide and the greatest increase in caspase 3 activity. Additionally, the percentage of phosphorylated Akt reached a minimum after 6 h of incubation. These results provide evidences that sperm death during in vitro incubation is largely an apoptotic phenomena, probably stimulated by endogenous production of hydrogen peroxide and the lack of prosurvival factors maintaining Akt in a phosphorylated status. Disclosing molecular mechanisms leading to sperm death may help to develop new strategies for stallion sperm conservation.
Impact of Probing the Reproductive Tract During Early Pregnancy on Fertility of Beef Cows
Authors: Pugliesi G , Scolari SC , Mesquita FS , Maturana Filho M , Araújo ER , Cardoso D , Sales JN , Martin I , Sá Filho M , Bertan CM , Binelli M 
Published: June 2014

ContentsThis short communication reports the impact of endometrial biopsies, uterine flushings and follicular fluid aspiration procedures at day 6 post artificial insemination (AI) on pregnancy rates. In Experiment 1, cows were timed AI (TAI) and assigned to the following treatment groups: control (n = 37), uterine flushing (n = 35) and endometrial biopsy (n = 38). On day 30 post AI, pregnancy rates were 40.5%, 33% and 28.5%, respectively (p > 0.1). Pregnancy rate on day 60 was lower (p < 0.004) in flushed cows than in the controls. In Experiment 2, oestrus was detected and cows were assigned to flushing (n = 32) or biopsy (n = 33) treatments 6 days after AI, which resulted in pregnancy rates of 31% and 36%, respectively (p > 0.1). In Experiment 3, cows were, 6 days after TAI, randomly assigned to the following treatments: control (n = 84) or aspiration of the largest follicle (n = 73). Pregnancy rates on day 30 post AI were 63.5% for the control group and 53% for the aspirated group (p > 0.1). In conclusion, uterine flushing and endometrial biopsy negatively affect pregnancy rates, but neither procedure can be considered to be incompatible with pregnancy maintenance. Follicular aspiration during pregnancy does not interact with pregnancy success. The amount and quality of samples obtained are compatible with the use of cellular and molecular analysis of uterine variables from cows that failed or succeeded on maintaining pregnancy.
The ARID‐HMG DNA‐binding protein AtHMGB15 is required for pollen tube growth in Arabidopsis thaliana
Authors: Xia Chuan , Wang Yu‐Jiao , Liang Yan , Niu Qian‐Kun , Tan Xiao‐Yun , Chu Liang‐Cui , Chen Li‐Qun , Zhang Xue‐Qin , Ye De 
Published: June 2014

SummaryIn flowering plants, male gametes (sperm cells) develop within male gametophytes (pollen grains) and are delivered to female gametes for double fertilization by pollen tubes. Therefore, pollen tube growth is crucial for reproduction. The mechanisms that control pollen tube growth remain poorly understood. In this study, we demonstrated that the ARID‐HMG DNA‐binding protein AtHMGB15 plays an important role in pollen tube growth. This protein is preferentially expressed in pollen grains and pollen tubes and is localized in the vegetative nuclei of the tricellular pollen grains and pollen tubes. Knocking down AtHMGB15 expression via a Ds insertion caused retarded pollen tube growth, leading to a significant reduction in the seed set. The athmgb15‐1 mutation affected the expression of 1686 genes in mature pollen, including those involved in cell wall formation and modification, cell signaling and cellular transport during pollen tube growth. In addition, it was observed that AtHMGB15 binds to DNA in vitro and interacts with the transcription factors AGL66 and AGL104, which are required for pollen maturation and pollen tube growth. These results suggest that AtHMGB15 functions in pollen tube growth through the regulation of gene expression.
Functional diversification of duplicated CYC2 clade genes in regulation of inflorescence development in Gerbera hybrida (Asteraceae)
Authors: Juntheikki‐Palovaara Inka , Tähtiharju Sari , Lan Tianying , Broholm Suvi K. , Rijpkema Anneke S. , Ruonala Raili , Kale Liga , Albert Victor A. , Teeri Teemu H. , Elomaa Paula 
Published: June 2014

SummaryThe complex inflorescences (capitula) of Asteraceae consist of different types of flowers. In Gerbera hybrida (gerbera), the peripheral ray flowers are bilaterally symmetrical and lack functional stamens while the central disc flowers are more radially symmetrical and hermaphroditic. Proteins of the CYC2 subclade of the CYC/TB1‐like TCP domain transcription factors have been recruited several times independently for parallel evolution of bilaterally symmetrical flowers in various angiosperm plant lineages, and have also been shown to regulate flower‐type identity in Asteraceae. The CYC2 subclade genes in gerbera show largely overlapping gene expression patterns. At the level of single flowers, their expression domain in petals shows a spatial shift from the dorsal pattern known so far in species with bilaterally symmetrical flowers, suggesting that this change in expression may have evolved after the origin of Asteraceae. Functional analysis indicates that GhCYC2, GhCYC3 and GhCYC4 mediate positional information at the proximal–distal axis of the inflorescence, leading to differentiation of ray flowers, but that they also regulate ray flower petal growth by affecting cell proliferation until the final size and shape of the petals is reached. Moreover, our data show functional diversification for the GhCYC5 gene. Ectopic activation of GhCYC5 increases flower density in the inflorescence, suggesting that GhCYC5 may promote the flower initiation rate during expansion of the capitulum. Our data thus indicate that modification of the ancestral network of TCP factors has, through gene duplications, led to the establishment of new expression domains and to functional diversification.
Gene coexpression patterns during early development of the native Arabidopsis reproductive meristem: novel candidate developmental regulators and patterns of functional redundancy
Authors: Mantegazza Otho , Gregis Veronica , Chiara Matteo , Selva Caterina , Leo Giulia , Horner David S. , Kater Martin M. 
Published: June 2014

SummaryDuring very early stages of flower development in Arabidopsis thaliana, a series of key decisions are taken. Indeed, the position and the basic patterning of new flowers are determined in less than 4 days. Given that the scientific literature provides hard evidence for the function of only 10% of A. thaliana genes, we hypothesized that although many essential genes have already been identified, many poorly characterized genes are likely to be involved in floral patterning. In the current study, we use high‐throughput sequencing to describe the transcriptome of the native inflorescence meristem, the floral meristem and the new flower immediately after the start of organ differentiation. We provide evidence that our experimental system is reliable and less affected by experimental artefacts than a widely used floral induction system. Furthermore, we show how these data can be used to identify candidate genes for functional studies, and to generate hypotheses of functional redundancies and regulatory interactions.
Accuracy of cytology in distinguishing adrenocortical tumors from pheochromocytoma in companion animals
Authors: Bertazzolo Walter , Didier Martine , Gelain Maria Elena , Rossi Silvia , Crippa Luca , Avallone Giancarlo , Roccabianca Paola , Bonfanti Ugo , Giori Luca , Fracassi Federico 
Published: June 2014

BackgroundThe distinction between adrenocortical tumors and pheochromocytoma can be challenging using clinical findings, diagnostic imaging and laboratory tests. Cytology might be a simple, minimally invasive method to reach a correct diagnosis.ObjectivesThe purpose of this study was to assess the accuracy of cytology in differentiating cortical from medullary tumors of the adrenal glands in dogs and cats.MethodsCytologic key features of adrenocortical tumors and pheochromocytoma were defined by one reference author. Cytologic specimens from primary adrenal tumors were submitted to 4 cytopathologists who were asked to classify the tumors based on the previously defined key features without knowledge of previous classification.ResultsTwenty specimens from histologically confirmed adrenal tumors (Group 1) and 4 specimens from adrenal tumors causing adrenal‐dependent Cushing's syndrome (Group 2) were evaluated by the 4 cytopathologists. Accuracy in differentiating cortical from medullary origin ranged from 90% to 100%, with a Kappa coefficient of agreement between cytopathologists of 0.95.ConclusionsThe origin of an adrenal tumor can be easily determined by cytology alone in many cases. However, cytology was not reliable in distinguishing benign from malignant neoplasia. Additional studies are needed to assess possible risks and complications associated with fine‐needle biopsy of adrenal tumors in dogs and cats.
Yersinia pseudotuberculosis ST42 (O:1) Strain Misidentified as Yersinia pestis by Mass Spectrometry Analysis
Authors: Gérôme Patrick , Le Flèche Philippe , Blouin Yann , Scholz Holger C. , Thibault François M. , Raynaud Françoise , Vergnaud Gilles , Pourcel Christine 
Published: June 2014

ABSTRACT

We report here the draft sequence of strain CEB14_0017, alias HIAD_DUP, recovered from a human patient and initially identified as
Yersinia pestis
by mass spectrometry analysis. Genotyping based on tandem repeat polymorphism assigned the strain to
Yersinia pseudotuberculosis
sequence type 42 (ST42). The total assembly length is 4,894,739 bp.
Draft Genome Sequence of Insecticidal
Streptomyces
sp. Strain PCS3-D2, Isolated from Mangrove Soil in Philippines
Authors: Bayot-Custodio Aileen N. , Alcantara Edwin P. , Zulaybar Teofila O. 
Published: June 2014

ABSTRACT

A draft genome sequence of a
Streptomyces
sp. isolated from mangrove soil in Cebu, Philippines, is described here. This isolate produced compounds with contact insecticidal activity against important corn pests. The genome contains 7,479,793 bp (in 27 scaffolds), 6,297 predicted genes, and 29 secondary metabolite biosynthetic gene clusters.
Complete Genome Sequence of Foot-and-Mouth Disease Virus Type A Circulating in Bangladesh
Authors: Ullah Huzzat , Siddique Mohammad Anwar , Sultana Munawar , Hossain M. Anwar 
Published: June 2014

ABSTRACT
The complete genome sequence of a foot-and-and mouth disease virus (FMDV) type A strain (BAN/GA/Sa-197/2013), isolated from Gazipur in Bangladesh, revealed an 84-nucleotide insertion within the 5′-untranslated region (UTR), a lengthened poly(C) tract, and amino acid substitutions at the VP1 region compared to the available genome sequence of the vaccine strain (GenBank accession no. HM854025).
Draft Genome Sequence of Photobacterium halotolerans S2753, Producer of Bioactive Secondary Metabolites
Authors: Machado Henrique , Månsson Maria , Gram Lone 
Published: June 2014

ABSTRACT

We report here the whole draft genome sequence of marine isolate
Photobacterium halotolerans
S2753, which produces the known antibiotic holomycin and also ngercheumicins and solonamides A and B, which interfere with virulence of methicillin-resistant
Staphylococcus aureus
strains by interacting with the quorum-sensing system.
Draft Genome Sequence of
Colletotrichum sublineola
, a Destructive Pathogen of Cultivated Sorghum
Authors: Baroncelli Riccardo , Sanz-Martín José María , Rech Gabriel E. , Sukno Serenella A. , Thon Michael R. 
Published: June 2014

ABSTRACT

Colletotrichum sublineola
is a filamentous fungus that causes anthracnose disease on sorghum. We report a draft whole-genome shotgun sequence and gene annotation of the nuclear genome of this fungus using Illumina sequencing.
Draft Genome Sequences of Two Genetic Variant Strains of
Edwardsiella piscicida
, JF1305 and RSB1309, Isolated from Olive Flounder (
Paralichythys olivaceus
) and Red Sea Bream (
Pagrus major
) Cultured in Japan, Respectively
Authors: Oguro Kazuki , Tamura Kazuki , Yamane Jin , Shimizu Masato , Yamamoto Takeshi , Ikawa Takuya , Ohnishi Kouhei , Oshima Syun-ichirou , Imajoh Masayuki 
Published: June 2014

ABSTRACT

Edwardsiella piscicida
is a new species discovered within the group of organisms traditionally classified as
Edwardsiella tarda
. We present draft genome sequences of two variant strains of
E. piscicida
, JF1305 and RSB1309. Differences in protein-coding sequence between these isolates are associated with virulence, disease, and defense, suggesting differences in pathogenicity.
Genome Sequence of Thermoanaerobaculum aquaticum MP-01
T
, the First Cultivated Member of
Acidobacteria
Subdivision 23, Isolated from a Hot Spring
Authors: Stamps Blake W. , Losey Nathaniel A. , Lawson Paul A. , Stevenson Bradley S. 
Published: June 2014

ABSTRACT

Thermoanaerobaculum aquaticum
MP-01
T
is currently the only cultivated and described member of
Acidobacteria
subdivision 23. Here, we report the genome sequence for this novel microorganism that was isolated from a hot spring.
Draft Genome Sequence of Aeromonas hydrophila Strain Ae34, Isolated from a Septicemic and Moribund Koi Carp (
Cyprinus carpio koi
), a Freshwater Aquarium Fish
Authors: Jagoda S. S. S. De S. , Tan Engkong , Arulkanthan Appudurai , Kinoshita Shigeharu , Watabe Shugo , Asakawa Shuichi 
Published: June 2014

ABSTRACT

Aeromonas hydrophila
is an important opportunistic pathogen that infects a variety of aquatic and terrestrial animals, including humans. We report here the draft genome sequence of
A. hydrophila
Ae34, a multidrug-resistant isolate from the kidney of a moribund koi carp (
Ciprinus carpio koi
) with signs of hemorrhagic septicemia.
Subclinical atherosclerosis and silent myocardial ischaemia in patients with type 2 diabetes: a protocol of a clinico-observational study
Authors: Prasad D S , Kabir Zubair , Devi K Revathi , Dash A K , Das B C 
Published: June 2014

IntroductionAtherosclerotic cardiovascular disease is a significant modifiable complication in patients with diabetes and subclinical atherosclerosis is considered a surrogate marker of future vascular events. The clustering of cardiometabolic-risk factors in patients with diabetes and cardiovascular disease is increasingly being recognised. Recent evidence indicates that 20–50% of asymptomatic patients with diabetes may have silent coronary heart disease. However, the identification of subclinical atherosclerosis and silent myocardial ischaemia in patients with diabetes has been less well-explored, especially in low-resource population settings where cost-effective non-invasive clinical tools are available. The objective of this study is to identify patients with physician-diagnosed diabetes who are at risk of developing future cardiovascular events measured as subclinical atherosclerosis and silent myocardial ischaemia in an urban population of Eastern India.Methods and analysisThis is a cross-sectional clinico-observational study. A convenience sampling of approximately 350 consecutive patients with type 2 diabetes based on predefined inclusion and exclusion criteria will be identified at an urban diabetes center. This estimated sample size is based on an expected prevalence of silent myocardial ischaemia of 25% (± 5%), we computed the required sample size using OpenEpi online software assuming an α level of 0.05 (95% CI) to be 289. On factoring 20% non-response the estimated sample size is 350. Previously validated questionnaire tools and well-defined clinical, anthropometric and biochemical measurements will be utilised for data collection. The two primary outcomes—subclinical atherosclerosis and silent myocardial ischaemia will be measured using carotid intima-media thickness and exercise tolerance testing, respectively. Descriptive and multivariate logistic regression statistical techniques will be employed to identify ‘at risk’ patients with diabetes, and adjusted for potential confounders.Ethics and disseminationEthical approval was granted by the institutional review board of Kalinga Institute of Medical Sciences, Bhubaneshwar, India. Data will be presented at academic fora and published in peer-reviewed journals.
First record of the pterosaur footprint
Pteraichnus
from the Saltwick Formation (Aalenian) of the Cleveland Basin, Yorkshire, UK
Authors: Whyte M. A. , Romano M. 
Published: June 2014

Summary

Prints belonging to
Pteraichnus
are recorded and described from the Saltwick Formation (Middle Jurassic, Aalenian Stage) at Hayburn Wyke on the Cleveland Coast of Yorkshire, England. This is the first record of
Pteraichnus
from the region and from the British Isles, and is an important addition to its diverse vertebrate ichnofauna. It is also only the second record of pterosaur footprints from the British Isles and is the oldest known occurrence of
Pteraichnus
. Significantly, it suggests that the pterodactyloid pterosaurs evolved earlier than has previously been supposed.