bluuebunny/crossref_metadata_2025_split huggingface dataset:
SNP variation in the promoter of the PRKAG3gene and association with meat quality traits in pig
Authors: Ryan Marion T , Hamill Ruth M , O’Halloran Aisling M , Davey Grace C , McBryan Jean , Mullen Anne M , McGee Chris , Gispert Marina , Southwood Olwen I , Sweeney Torres 
Published: July 2012

Abstract

Background
The PRKAG3 gene encodes the γ3 subunit of adenosine monophosphate activated protein kinase (AMPK), a protein that plays a key role in energy metabolism in skeletal muscle. Non-synonymous single nucleotide polymorphisms (SNPs) in this gene such as I199V are associated with important pork quality traits. The objective of this study was to investigate the relationship between gene expression of the PRKAG3 gene, SNP variation in the PRKAG3 promoter and meat quality phenotypes in pork.

Results

PRKAG3 gene expression was found to correlate with a number of traits relating to glycolytic potential (GP) and intramuscular fat (IMF) in three phenotypically diverse F1 crosses comprising of 31 Large White, 23 Duroc and 32 Pietrain sire breeds. The majority of associations were observed in the Large White cross. There was a significant association between genotype at the g.-311A>G locus and PRKAG3 gene expression in the Large White cross. In the same population, ten novel SNPs were identified within a 1.3 kb region spanning the promoter and from this three major haplotypes were inferred. Two tagging SNPs (g.-995A>G and g.-311A>G) characterised the haplotypes within the promoter region being studied. These two SNPs were subsequently genotyped in larger populations consisting of Large White (n = 98), Duroc (n = 99) and Pietrain (n = 98) purebreds. Four major haplotypes including promoter SNP’s g.-995A>G and g.-311A>G and I199V were inferred. In the Large White breed, HAP1 was associated with IMF% in the M. longissmus thoracis et lumborum (LTL) and driploss%. HAP2 was associated with IMFL% GP-influenced traits pH at 24 hr in LTL (pHULT), pH at 45 min in LTL (pH45LT) and pH at 45 min in the M. semimembranosus muscle (pH45SM). HAP3 was associated with driploss%, pHULT pH45LT and b* Minolta. In the Duroc breed, associations were observed between HAP1 and driploss% and pHUSM. No associations were observed with the remaining haplotypes (HAP2, HAP3 and HAP4) in the Duroc breed. The Pietrain breed was monomorphic in the promoter region. The I199V locus was associated with several GP-influenced traits across all three breeds and IMF% in the Large White and Pietrain breed. No significant difference in promoter function was observed for the three main promoter haplotypes when tested in vitro.

Conclusion
Gene expression levels of the porcine PRKAG3 are associated with meat quality phenotypes relating to glycolytic potential and IMF% in the Large White breed, while SNP variation in the promoter region of the gene is associated with PRKAG3 gene expression and meat quality phenotypes.
Indication for Co-evolution of Lactobacillus johnsonii with its hosts
Authors: Buhnik-Rosenblau Keren , Matsko-Efimov Vera , Jung Minju , Shin Heuynkil , Danin-Poleg Yael , Kashi Yechezkel 
Published: July 2012

Abstract

Background
The intestinal microbiota, composed of complex bacterial populations, is host-specific and affected by environmental factors as well as host genetics. One important bacterial group is the lactic acid bacteria (LAB), which include many health-promoting strains. Here, we studied the genetic variation within a potentially probiotic LAB species, Lactobacillus johnsonii, isolated from various hosts.

Results
A wide survey of 104 fecal samples was carried out for the isolation of L. johnsonii. As part of the isolation procedure, terminal restriction fragment length polymorphism (tRFLP) was performed to identify L. johnsonii within a selected narrow spectrum of fecal LAB. The tRFLP results showed host specificity of two bacterial species, the Enterococcus faecium species cluster and Lactobacillus intestinalis, to different host taxonomic groups while the appearance of L. johnsonii and E. faecalis was not correlated with any taxonomic group. The survey ultimately resulted in the isolation of L. johnsonii from few host species. The genetic variation among the 47 L. johnsonii strains isolated from the various hosts was analyzed based on variation at simple sequence repeats (SSR) loci and multi-locus sequence typing (MLST) of conserved hypothetical genes. The genetic relationships among the strains inferred by each of the methods were similar, revealing three different clusters of L. johnsonii strains, each cluster consisting of strains from a different host, i.e. chickens, humans or mice.

Conclusions
Our typing results support phylogenetic separation of L. johnsonii strains isolated from different animal hosts, suggesting specificity of L. johnsonii strains to their hosts. Taken together with the tRFLP results, that indicated the association of specific LAB species with the host taxonomy, our study supports co-evolution of the host and its intestinal lactic acid bacteria.
PIM-1 kinase interacts with the DNA binding domain of the vitamin D receptor: a further kinase implicated in 1,25-(OH)2D3 signaling
Authors: Maier Christina J , Maier Richard H , Rid Raphaela , Trost Andrea , Hundsberger Harald , Eger Andreas , Hintner Helmut , Bauer Johann W , Onder Kamil 
Published: July 2012

Abstract

Background
The vitamin D3 receptor (VDR) is responsible for mediating the pleiotropic and, in part, cell-type-specific effects of 1,25-dihydroxyvitamin D3 (calcitriol) on the cardiovascular and the muscle system, on the bone development and maintenance, mineral homeostasis, cell proliferation, cell differentiation, vitamin D metabolism, and immune response modulation.

Results
Based on data obtained from genome-wide yeast two-hybrid screenings, domain mapping studies, intracellular co-localization approaches as well as reporter transcription assay measurements, we show here that the C-terminus of human PIM-1 kinase isoform2 (amino acid residues 135–313), a serine/threonine kinase of the calcium/calmodulin-regulated kinase family, directly interacts with VDR through the receptor’s DNA-binding domain. We further demonstrate that PIM-1 modulates calcitriol signaling in HaCaT keratinocytes by enhancing both endogenous calcitriol response gene transcription (osteopontin) and an extrachromosomal DR3 reporter response.

Conclusion
These results, taken together with previous reports of involvement of kinase pathways in VDR transactivation, underscore the biological relevance of this novel protein-protein interaction.
Medication coaching program for patients with minor stroke or TIA: A pilot study
Authors: Sides Elizabeth G , Zimmer Louise O , Wilson Leslie , Pan Wenqin , Olson DaiWai M , Peterson Eric D , Bushnell Cheryl 
Published: July 2012

AbstractBackgroundPatients who are hospitalized with a first or recurrent stroke often are discharged with new medications or adjustment to the doses of pre-admission medications, which can be confusing and pose safety issues if misunderstood. The purpose of this pilot study was to assess the feasibility of medication coaching via telephone after discharge in patients with stroke.MethodsTwo-arm pilot study of a medication coaching program with 30 patients (20 intervention, 10 control). Consecutive patients admitted with stroke or TIA with at least 2 medications changed between admission and discharge were included. The medication coach contacted intervention arm patients post-discharge via phone call to discuss risk factors, review medications and triage patients’ questions to a stroke nurse and/or pharmacist. Intervention and control participants were contacted at 3 months for outcomes. The main outcomes were feasibility (appropriateness of script, ability to reach participants, and provide requested information) and participant evaluation of medication coaching.ResultsThe median lengths of the coaching and follow-up calls with requested answers to these questions were 27 minutes and 12 minutes, respectively, and participant evaluations of the coaching were positive. The intervention participants were more likely to have seen their primary care provider than were control participants by 3 months post discharge.ConclusionsThis medication coaching study executed early after discharge demonstrated feasibility of coaching and educating stroke patients with a trained coach. Results from our small pilot showed a possible trend towards improved appointment-keeping with primary care providers in those who received coaching.
Associations between fruit and vegetable intake, leisure-time physical activity, sitting time and self-rated health among older adults: cross-sectional data from the WELL study
Authors: Södergren Marita , McNaughton Sarah A , Salmon Jo , Ball Kylie , Crawford David A 
Published: July 2012

Abstract

Background
Lifestyle behaviours, such as healthy diet, physical activity and sedentary behaviour, are key elements of healthy ageing and important modifiable risk factors in the prevention of chronic diseases. Little is known about the relationship between these behaviours in older adults. The purpose of this study was to explore the relationship between fruit and vegetable (F&V) intake, leisure-time physical activity (LTPA) and sitting time (ST), and their association with self-rated health in older adults.

Methods
This cross-sectional study comprised 3,644 older adults (48% men) aged 55–65 years, who participated in the Wellbeing, Eating and Exercise for a Long Life (“WELL”) study. Respondents completed a postal survey about their health and their eating and physical activity behaviours in 2010 (38% response rate). Spearman’s coefficient (rho) was used to evaluate the relationship between F&V intake, LTPA and ST. Their individual and shared associations with self-rated health were examined using ordinal logistic regression models, stratified by sex and adjusted for confounders (BMI, smoking, long-term illness and socio-demographic characteristics).

Results
The correlations between F&V intake, LTPA and ST were low. F&V intake and LTPA were positively associated with self-rated health. Each additional serving of F&V or MET-hour of LTPA were associated with approximately 10% higher likelihood of reporting health as good or better among women and men. The association between ST and self-rated health was not significant in the multivariate analysis. A significant interaction was found (ST*F&V intake). The effect of F&V intake on self-rated health increased with increasing ST in women, whereas the effect decreased with increasing ST in men.

Conclusions
This study contributes to the scarce literature related to lifestyle behaviours and their association with health indicators among older adults. The findings suggest that a modest increase in F&V intake, or LTPA could have a marked effect on the health of older adults. Further research is needed to fully understand the correlates and determinants of lifestyle behaviours, particularly sitting time, in this age group.
Inhibition of Phosphodiesterase-4 (PDE4) activity triggers luminal apoptosis and AKT dephosphorylation in a 3-D colonic-crypt model
Authors: Tsunoda Toshiyuki , Ota Takeharu , Fujimoto Takahiro , Doi Keiko , Tanaka Yoko , Yoshida Yasuhiro , Ogawa Masahiro , Matsuzaki Hiroshi , Hamabashiri Masato , Tyson Darren R , Kuroki Masahide , Miyamoto Shingo , Shirasawa Senji 
Published: July 2012

Abstract

Background
We previously established a three-dimensional (3-D) colonic crypt model using HKe3 cells which are human colorectal cancer (CRC) HCT116 cells with a disruption in oncogenic KRAS, and revealed the crucial roles of oncogenic KRAS both in inhibition of apoptosis and in disruption of cell polarity; however, the molecular mechanism of KRAS-induced these 3-D specific biological changes remains to be elucidated.

Results
Among the genes that were upregulated by oncogenic KRAS in this model, we focused on the phosphodiesterase 4B (PDE4B) of which expression levels were found to be higher in clinical tumor samples from CRC patients in comparison to those from healthy control in the public datasets of gene expression analysis. PDE4B2 was specifically overexpressed among other PDE4 isoforms, and re-expression of oncogenic KRAS in HKe3 cells resulted in PDE4B overexpression. Furthermore, the inhibition of PDE4 catalytic activity using rolipram reverted the disorganization of HCT116 cells into the normal physiologic state of the epithelial cell polarity by inducing the apical assembly of ZO-1 (a tight junction marker) and E-cadherin (an adherens junction marker) and by increasing the activity of caspase-3 (an apoptosis marker) in luminal cavities. Notably, rolipram reduced the AKT phosphorylation, which is known to be associated with the disruption of luminal cavity formation and CRC development. Similar results were also obtained using PDE4B2-shRNAs. In addition, increased expression of PDE4B mRNA was found to be correlated with relapsed CRC in a public datasets of gene expression analysis.

Conclusions
These results collectively suggested that PDE4B is upregulated by oncogenic KRAS, and also that the inhibition of PDE4 catalytic activity can induce both epithelial cell polarity and luminal apoptosis in CRC, thus highlighting the utility of our 3-D culture (3 DC) model for the KRAS-induced development of CRC in 3-D microenvironment. Indeed, using this model, we found that PDE4B is a promising candidate for a therapeutic target as well as prognostic molecular marker in CRC. Further elucidation of the signaling network of PDE4B2 in 3 DC would provide a better understanding of CRC in vivo.
On Fibonacci functions with Fibonacci numbers
Authors: Han Jeong Soon , Kim Hee Sik , Neggers Joseph 
Published: July 2012

Abstract
In this paper we consider Fibonacci functions on the real numbers R, i.e., functions

f
:
R
→
R

such that for all

x
∈
R

,

f
(
x
+
2
)
=
f
(
x
+
1
)
+
f
(
x
)

. We develop the notion of Fibonacci functions using the concept of f-even and f-odd functions. Moreover, we show that if f is a Fibonacci function then

lim

x
→
∞

f
(
x
+
1
)

f
(
x
)

=

1
+

5

2

.

MSC:11B39, 39A10.
An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data
Authors: Bozek Katarzyna , Eckhardt Manon , Sierra Saleta , Anders Maria , Kaiser Rolf , Kräusslich Hans-Georg , Müller Barbara , Lengauer Thomas 
Published: July 2012

AbstractBackgroundEntry of human immunodeficiency virus type 1 (HIV-1) into the host cell involves interactions between the viral envelope glycoproteins (Env) and the cellular receptor CD4 as well as a coreceptor molecule (most importantly CCR5 or CXCR4). Viral preference for a specific coreceptor (tropism) is in particular determined by the third variable loop (V3) of the Env glycoprotein gp120. The approval and use of a coreceptor antagonist for antiretroviral therapy make detailed understanding of tropism and its accurate prediction from patient derived virus isolates essential. The aim of the present study is the development of an extended description of the HIV entry phenotype reflecting its co-dependence on several key determinants as the basis for a more accurate prediction of HIV-1 entry phenotype from genotypic data.ResultsHere, we established a new protocol of quantitation and computational analysis of the dependence of HIV entry efficiency on receptor and coreceptor cell surface levels as well as viral V3 loop sequence and the presence of two prototypic coreceptor antagonists in varying concentrations. Based on data collected at the single-cell level, we constructed regression models of the HIV-1 entry phenotype integrating the measured determinants. We developed a multivariate phenotype descriptor, termed phenotype vector, which facilitates a more detailed characterization of HIV entry phenotypes than currently used binary tropism classifications. For some of the tested virus variants, the multivariant phenotype vector revealed substantial divergences from existing tropism predictions. We also developed methods for computational prediction of the entry phenotypes based on the V3 sequence and performed an extrapolating calculation of the effectiveness of this computational procedure.ConclusionsOur study of the HIV cell entry phenotype and the novel multivariate representation developed here contributes to a more detailed understanding of this phenotype and offers potential for future application in the effective administration of entry inhibitors in antiretroviral therapies.
Array CGH improves detection of mutations in the GALC gene associated with Krabbe disease
Authors: Tanner Alice K , Chin Ephrem L H , Duffner Patricia K , Hegde Madhuri 
Published: July 2012

Abstract

Background
Krabbe disease is an autosomal recessive lysosomal storage disorder caused by mutations in the GALC gene. The most common mutation in the Caucasian population is a 30-kb deletion of exons 11 through 17. There are few other reports of intragenic GALC deletions or duplications, due in part to difficulties detecting them.

Methods and results
We used gene-targeted array comparative genomic hybridization (CGH) to analyze the GALC gene in individuals with Krabbe disease in whom sequence analysis with 30-kb deletion analysis identified only one mutation. In our sample of 33 cases, traditional approaches failed to identify two pathogenic mutations in five (15.2%) individuals with confirmed Krabbe disease. The addition of array CGH deletion/duplication analysis to the genetic testing strategy led to the identification of a second pathogenic mutation in three (9.1%) of these five individuals. In all three cases, the deletion or duplication identified through array CGH was a novel GALC mutation, including the only reported duplication in the GALC gene, which would have been missed by traditional testing methodologies. We report these three cases in detail. The second mutation remains unknown in the remaining two individuals (6.1%), despite our full battery of testing.

Conclusions
Analysis of the GALC gene using array CGH deletion/duplication testing increased the two-mutation detection rate from 84.8% to 93.9% in affected individuals. Better mutation detection rates are important for improving molecular diagnosis of Krabbe disease, as well as for providing prenatal and carrier testing in family members.
Abrogated RANKL expression in properdin-deficient mice is associated with better outcome from collagen-antibody-induced arthritis
Authors: Dimitrova Petya , Ivanovska Nina , Belenska Lyudmila , Milanova Viktoriya , Schwaeble Wilhelm , Stover Cordula 
Published: July 2012

Abstract
Introduction
Properdin amplifies the alternative pathway of complement activation. In the present study, we evaluated its role in the development of collagen antibody-induced arthritis (CAIA).

Methods
Arthritis was induced by intraperitoneal injection of a collagen antibody cocktail into properdin-deficient (KO) and wild-type (WT) C57BL/6 mice. Symptoms of disease were evaluated daily. The degree of joint damage was assessed histologically and with immunostaining for bone-resorption markers. Phenotypes of cell populations, their receptor expression, and intracellular cytokine production were determined with flow cytometry. Osteoclast differentiation of bone marrow (BM) precursors was evaluated by staining for tartrate-resistant acid phosphatase (TRAP).

Results
Properdin-deficient mice developed less severe CAIA than did WT mice. They showed significantly improved clinical scores and downregulated expression of bone-resorption markers in the joints at day 10 of disease. The frequencies of Ly6G+CD11b+ cells were fewer in BM, blood, and synovial fluid (SF) of KO than of WT CAIA mice. The receptor activator of nuclear factor κB ligand (RANKL) was downregulated on arthritic KO neutrophils from BM and the periphery. Decreased C5a amounts in KO SF contributed to lower frequencies of CD5aR+-bearing neutrophils. In blood, surface C5aR was detected on KO Ly6G+ cells as a result of low receptor engagement. Circulating CD4+ T cells had an altered ability to produce interleukin (IL)-17 and interferon (IFN)-γ and to express RANKL. In KO CAIA mice, decreased frequencies of CD4+ T cells in the spleen were related to low CD86 expression on Ly6GhighCD11b+ cells. Arthritic KO T cells spontaneously secreted IFN-γ but not IL-17 and IL-6, and responded to restimulation with less-vigorous cytokine production in comparison to WT cells. Fewer TRAP-positive mature osteoclasts were found in KO BM cell cultures.

Conclusions
Our data show that the active involvement of properdin in arthritis is related to an increased proinflammatory cytokine production and RANKL expression on immune cells and to a stimulation of the RANKL-dependent osteoclast differentiation.
Spectral transmission of the principal-eye corneas of jumping spiders: implications for ultraviolet vision
Authors: Hu Zhiyong , Liu Fengxiang , Xu Xin , Chen Zhanqi , Chen Jian , Li Daiqin 
Published: July 2012

SUMMARYUltraviolet (UV) vision plays an important role in interspecific and intraspecific communication in many animals. However, UV vision and its adaptive significance have been investigated in only approximately 1% of more than 5000 species of jumping spiders (Araneae: Salticidae), renowned for their unique, complex eyes that support exceptional spatial acuity and visually based behaviour. To appreciate the adaptive significance of UV vision, it is important to establish whether salticids can perceive UV and whether the perception of UV varies with ecological factors such as light environment. In this study, we measured the UV-transmission properties of the principal-eye corneas of 128 salticid species. We found that the corneas of all measured species were able to transmit UV light, making the perception of UV possible. Three classes of corneal spectral transmission curves were identified; the majority of species had a Class II curve with a less-steep slope and a gradual onset of the transmission cut-off; all the remaining species had a Class I curve with a very steep slope and a sharp cut-off except for one species that had a Class III curve with an intermediate step, which appeared as a shoulder on the descending part of the transmission curve. The T50 cut-off transmission values (the wavelength at which 50% of the maximum transmission is reached) in salticid corneas vary with species and light habitat. The corneas of species inhabiting open bush had a higher relative transmission at short wavelengths in the UV than forest species. This is the first investigation of corneal transmission in spiders and suggests that UV perception is widespread in salticids.