bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSTPIP2 deficiency in mice causes osteopenia and increased differentiation of multipotent myeloid precursors into osteoclasts
Authors: Chitu Violeta , Nacu Viorel , Charles Julia F. , Henne William M. , McMahon Harvey T. , Nandi Sayan , Ketchum Halley , Harris Renee , Nakamura Mary C. , Stanley E. Richard 
Published: August 2012

AbstractMissense mutations that reduce or abrogate myeloid cell expression of the F-BAR domain protein, proline serine threonine phosphatase-interacting protein 2 (PSTPIP2), lead to autoinflammatory disease involving extramedullary hematopoiesis, skin and bone lesions. However, little is known about how PSTPIP2 regulates osteoclast development. Here we examined how PSTPIP2 deficiency causes osteopenia and bone lesions, using the mouse PSTPIP2 mutations, cmo, which fails to express PSTPIP2 and Lupo, in which PSTPIP2 is dysfunctional. In both models, serum levels of the pro-osteoclastogenic factor, MIP-1α, were elevated and CSF-1 receptor (CSF-1R)–dependent production of MIP-1α by macrophages was increased. Treatment of cmo mice with a dual specificity CSF-1R and c-Kit inhibitor, PLX3397, decreased circulating MIP-1α and ameliorated the extramedullary hematopoiesis, inflammation, and osteopenia, demonstrating that aberrant myelopoiesis drives disease. Purified osteoclast precursors from PSTPIP2-deficient mice exhibit increased osteoclastogenesis in vitro and were used to probe the structural requirements for PSTPIP2 suppression of osteoclast development. PSTPIP2 tyrosine phosphorylation and a functional F-BAR domain were essential for PSTPIP2 inhibition of TRAP expression and osteoclast precursor fusion, whereas interaction with PEST-type phosphatases was only required for suppression of TRAP expression. Thus, PSTPIP2 acts as a negative feedback regulator of CSF-1R signaling to suppress inflammation and osteoclastogenesis.
H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
Authors: Karmodiya Krishanpal , Krebs Arnaud R , Oulad-Abdelghani Mustapha , Kimura Hiroshi , Tora Laszlo 
Published: August 2012

Abstract

Background
Transcription regulation in pluripotent embryonic stem (ES) cells is a complex process that involves multitude of regulatory layers, one of which is post-translational modification of histones. Acetylation of specific lysine residues of histones plays a key role in regulating gene expression.

Results
Here we have investigated the genome-wide occurrence of two histone marks, acetylation of histone H3K9 and K14 (H3K9ac and H3K14ac), in mouse embryonic stem (mES) cells. Genome-wide H3K9ac and H3K14ac show very high correlation between each other as well as with other histone marks (such as H3K4me3) suggesting a coordinated regulation of active histone marks. Moreover, the levels of H3K9ac and H3K14ac directly correlate with the CpG content of the promoters attesting the importance of sequences underlying the specifically modified nucleosomes. Our data provide evidence that H3K9ac and H3K14ac are also present over the previously described bivalent promoters, along with H3K4me3 and H3K27me3. Furthermore, like H3K27ac, H3K9ac and H3K14ac can also differentiate active enhancers from inactive ones. Although, H3K9ac and H3K14ac, a hallmark of gene activation exhibit remarkable correlation over active and bivalent promoters as well as distal regulatory elements, a subset of inactive promoters is selectively enriched for H3K14ac.

Conclusions
Our study suggests that chromatin modifications, such as H3K9ac and H3K14ac, are part of the active promoter state, are present over bivalent promoters and active enhancers and that the extent of H3K9 and H3K14 acetylation could be driven by cis regulatory elements such as CpG content at promoters. Our study also suggests that a subset of inactive promoters is selectively and specifically enriched for H3K14ac. This observation suggests that histone acetyl transferases (HATs) prime inactive genes by H3K14ac for stimuli dependent activation. In conclusion our study demonstrates a wider role for H3K9ac and H3K14ac in gene regulation than originally thought.
SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure
Authors: Parida Swarup K , Mukerji Mitali , Singh Ashok K , Singh Nagendra K , Mohapatra Trilochan 
Published: August 2012

Abstract

Background
Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice.

Results
Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species.

Conclusions
SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice.
Precipitating and relieving factors of migraine versus tension type headache
Authors: Haque Badrul , Rahman Kazi Mohibur , Hoque Azharul , Hasan ATM Hasibul , Chowdhury Rajib Nayan , Khan Sharif Uddin , Alam Mondal Badrul , Habib Mansur , Mohammad Quazi Deen 
Published: August 2012

Abstract

Background
To determine the differences of precipitating and relieving factors between migraine and tension type headache.

Methods
This is a cross sectional study. We retrospectively reviewed the records of 250 migraine patients and 250 patients diagnosed as tension type headache from the specialized headache clinic in Dept. of Neurology, Dhaka Medical College Hospital. Data were collected through a predesigned questionnaire containing information on age, sex, social status and a predetermined list of precipitating and relieving factors.

Results
In this study, the female patients predominated (67%). Most of the patients were within 21–30 years age group (58.6%). About 58% of them belonged to middle class families. The common precipitating factors like stress, anxiety, activity, journey, reading, cold and warm were well distributed among both the migraine and tension type headache (TTH) patients. But significant difference was demonstrated for fatigue (p < 0.05), sleep deprivation (p < 0.05), sunlight (p < 0.01) and food (p < 0.05), which were common among migraineurs. In consideration of relieving factors of pain, different maneuvers were commonly tried by migraineurs and significant difference were observed for both analgesic drug and massage (p < 0.05), which relieved migraine headache. But maneuvers like sleep, rest and posture were used by both groups.

Conclusion
The most frequent precipitating factors for headache appear to be identical for both migraine and TTH patients. Even though some factors like fatigue, sleep deprivation, sunlight and food significantly precipitate migraine and drug, massage are effective maneuver for relieving pain among migrianeurs.
Different associations of white matter lesions with depression and cognition
Authors: Lee Jun-Young , Insel Philip , Mackin R Scott , Schuff Norbert , Chui Helena , DeCarli Charles , Park Kee Hyung , Mueller Susanne G , Weiner Michael W 
Published: August 2012

Abstract

Background
To test the hypothesis that white matter lesions (WML) are primarily associated with regional frontal cortical volumes, and to determine the mediating effects of these regional frontal cortices on the associations of WML with depressive symptoms and cognitive dysfunction.

Methods
Structural brains MRIs were performed on 161 participants: cognitively normal, cognitive impaired but not demented, and demented participants. Lobar WML volumes, regional frontal cortical volumes, depressive symptom severity, and cognitive abilities were measured. Multiple linear regression analyses were used to identify WML volume effects on frontal cortical volume. Structural equation modeling was used to determine the MRI-depression and the MRI-cognition path relationships.

Results
WML predicted frontal cortical volume, particularly in medial orbirtofrontal cortex, irrespective of age, gender, education, and group status. WML directly predicted depressive score, and this relationship was not mediated by regional frontal cortices. In contrast, the association between WML and cognitive function was indirect and mediated by regional frontal cortices.

Conclusions
These findings suggest that the neurobiological mechanisms underpinning depressive symptoms and cognitive dysfunction in older adults may differ.
Current status and emerging role of glutathione in food grade lactic acid bacteria
Authors: Pophaly Sarang Dilip , Singh Rameshwar , Pophaly Saurabh Dilip , Kaushik Jai K , Tomar Sudhir Kumar 
Published: August 2012

Abstract
Lactic acid bacteria (LAB) have taken centre stage in perspectives of modern fermented food industry and probiotic based therapeutics. These bacteria encounter various stress conditions during industrial processing or in the gastrointestinal environment. Such conditions are overcome by complex molecular assemblies capable of synthesizing and/or metabolizing molecules that play a specific role in stress adaptation. Thiols are important class of molecules which contribute towards stress management in cell. Glutathione, a low molecular weight thiol antioxidant distributed widely in eukaryotes and Gram negative organisms, is present sporadically in Gram positive bacteria. However, new insights on its occurrence and role in the latter group are coming to light. Some LAB and closely related Gram positive organisms are proposed to possess glutathione synthesis and/or utilization machinery. Also, supplementation of glutathione in food grade LAB is gaining attention for its role in stress protection and as a nutrient and sulfur source. Owing to the immense benefits of glutathione, its release by probiotic bacteria could also find important applications in health improvement. This review presents our current understanding about the status of glutathione and its role as an exogenously added molecule in food grade LAB and closely related organisms.
Modulation of ovine SBD-1 expression by 17beta-estradiol in ovine oviduct epithelial cells
Authors: Wen Shiyong , Cao Guifang , Bao Tuya , Cheng LanLing , Li Haijun , Du Chenguang , Tu Yong , Li Qi , Jian Ruizhen , Zhao Pengwei ,   Wuriliga
Published: August 2012

AbstractBackgroundMucosal epithelia, including those of the oviduct, secrete antimicrobial innate immune molecules (AIIMS). These have bactericidal/bacteriostatic functions against a variety of pathogens. Among the AIIMs, sheep β-defensin-1 (SBD-1) is one of the most potent. Even though the SBD-1 is an important AIIM and it is regulated closely by estrogenic hormone, the regulation mechanism of 17β-estradiol has not been clearly established. We investigated the effects of E2and agonist or inhibitor on ovine oviduct epithelial cells in regard to SBD-1 expression using reverse transcription quantitative PCR (RT-qPCR). In addition, three different pathways were inhibited separately or simultaneously to confirm the effect of different inhibitors in the regulation mechanism.Results17beta-estradiol (E2) induced release of SBD-1 in ovine oviduct epithelial cells. SBD-1 expression was mediated through G-protein-coupled receptor 30 (GPR30) and Estrogen Receptors (ERs) activation in ovine oviduct epithelial cell. Inhibition of gene expression of protein kinase A (PKA), protein kinase C (PKC), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) led to a decreased SBD-1 expression.ConclusionsTaken together, E2-induced up-regulation of SBD-1 expressions were GPR30-dependent during prophase and ERs-dependent during later-stage in ovine oviduct epithelial cells, and we assume that the effect was completed by the PKA, PKC, and NF-κB pathways simultaneous.
Topological effects of data incompleteness of gene regulatory networks
Authors: Sanz Joaquin , Cozzo Emanuele , Borge-Holthoefer Javier , Moreno Yamir 
Published: August 2012

Abstract

Background
The topological analysis of biological networks has been a prolific topic in network science during the last decade. A persistent problem with this approach is the inherent uncertainty and noisy nature of the data. One of the cases in which this situation is more marked is that of transcriptional regulatory networks (TRNs) in bacteria. The datasets are incomplete because regulatory pathways associated to a relevant fraction of bacterial genes remain unknown. Furthermore, direction, strengths and signs of the links are sometimes unknown or simply overlooked. Finally, the experimental approaches to infer the regulations are highly heterogeneous, in a way that induces the appearance of systematic experimental-topological correlations. And yet, the quality of the available data increases constantly.

Results
In this work we capitalize on these advances to point out the influence of data (in)completeness and quality on some classical results on topological analysis of TRNs, specially regarding modularity at different levels.

Conclusions
In doing so, we identify the most relevant factors affecting the validity of previous findings, highlighting important caveats to future prokaryotic TRNs topological analysis.
Diverse modulation of spa transcription by cell wall active antibiotics in Staphylococcus aureus
Authors: Nielsen Lene N , Roggenbuck Michael , Haaber Jakob , Ifrah Dan , Ingmer Hanne 
Published: August 2012

Abstract

Background
The aim of this study was to investigate the effect of various classes of clinically relevant antibiotics at sub-lethal concentrations on virulence gene expression and biofilm formation in Staphylococcus aureus.

Findings

LacZ promoter fusions of genes related to staphylococcal virulence were used to monitor the effects of antibiotics on gene expression in a disc diffusion assay. The selected genes were hla and spa encoding α-hemolysin and Protein A, respectively and RNAIII, the effector molecule of the agr quorum sensing system. The results were confirmed by quantitative real-time PCR. Additionally, we monitored the effect of subinhibitory concentrations of antibiotics on the ability of S. aureus to form biofilm in a microtiter plate assay. The results show that sub-lethal antibiotic concentrations diversely modulate expression of RNAIII, hla and spa. Consistently, expression of all three genes were repressed by aminoglycosides and induced by fluoroquinolones and penicillins. In contrast, the β-lactam sub-group cephalosporins enhanced expression of RNAIII and hla but diversely affected expression of spa. The compounds cefalotin, cefamandole, cefoxitin, ceftazidime and cefixine were found to up-regulate spa, while down-regulation was observed for cefuroxime, cefotaxime and cefepime. Interestingly, biofilm assays demonstrated that the spa-inducing cefalotin resulted in less biofilm formation compared to the spa-repressing cefotaxime.

Conclusions
We find that independently of the cephalosporin generation, cephalosporins oppositely regulate spa expression and biofilm formation. Repression of spa expression correlates with the presence of a distinct methyloxime group while induction correlates with an acidic substituted oxime group. As cephalosporines target the cell wall penicillin binding proteins we speculate that subtle differences in this interaction fine-tunes spa expression independently of agr.
Membrane microdomain-associated uroplakin IIIa contributes to Src-dependent mechanisms of anti-apoptotic proliferation in human bladder carcinoma cells
Authors: Kihira Shigeru , Yoshida Junpei , Kawada Yukari , Hitomi Yuriko , Asada Tomohisa , Hisatomi Rie , Ohta Akina , Iwasaki Tetsushi , Mahbub Hasan A. K. M. , Fukami Yasuo , Sato Ken-ichi 
Published: August 2012

Summary
Our previous study demonstrated that tyrosine phosphorylation of p145met/β-subunit of hepatocyte growth factor receptor by epidermal growth factor receptor and Src contributes to the anti-apoptotic growth of human bladder carcinoma cell 5637 under serum-starved conditions. Here, we show that some other cell lines of human bladder carcinoma, but not other types of human cancer cells, also exhibit Src-dependent, anti-apoptotic proliferation under serum-starved conditions, and that low-density, detergent-insoluble membrane microdomains (MD) serve as a structural platform for signaling events involving p145met, EGFR, and Src. As an MD-associated molecule that may contribute to bladder carcinoma-specific cellular function, we identified uroplakin IIIa (UPIIIa), an urothelium-specific protein. Results obtained so far revealed: 1) UPIIIa undergoes partial proteolysis in serum-starved cells; 2) a specific antibody to the extracellular domain of UPIIIa inhibits the proteolysis of UPIIIa and the activation of Src, and promotes apoptosis in serum-starved cells; and 3) knockdown of UPIIIa by short interfering RNA also promotes apoptosis in serum-starved cells. GM6001, a potent inhibitor of matrix metalloproteinase (MMP), inhibits the proteolysis of UPIIIa and promotes apoptosis in serum-starved cells. Furthermore, serum starvation promotes expression and secretion of the heparin-binding EGF-like growth factor in a manner that depends on the functions of MMP, Src, and UPIIIa. These results highlight a hitherto unknown signaling network involving a subset of MD-associated molecules in the anti-apoptotic mechanisms of human bladder carcinoma cells.
Preparation for elective colorectal surgery using a video: a questionnaire-based observational study
Authors: Ihedioha U , Sangal S , Mastermann J , Singh B , Chaudhri S 
Published: August 2012

Objective Every patient has a perception about surgery and psychological preparation of the patient has an important impact on their postoperative recovery and outcome. In this study we looked at impact of a visual educational aid, in the form of a patient DVD on outcome following colorectal surgery within an enhanced recovery programme (ERP). Design We carried out a prospective analysis of a consecutive series of patients undergoing elective colorectal resection. All patients were given information about their operation in a clinic setting. Our intervention included a 15 minute patient educational video describing the preoperative assessment, post-operative recovery and advice on discharge. A questionnaire on patients’ views of ERP and video education was given on discharge. Setting University teaching hospital Participants Patients undergoing elective colorectal resection Main Outcome Measures Outcomes studied included length of hospital stay, patient perception of ERP, postoperative complications and readmissions: Results Thirty-two patients underwent elective colorectal surgery over a 3 month period. Median length of stay in hospital was 5 days. The questionnaire response rate was 100%. All patients thought they were well informed of the enhanced recovery programme. Eighty-eight percent responded that the video information provided about their operation was adequate, with 28% finding the video very helpful and more useful than other forms of patient information. There were no major postoperative complications and no readmissions. Conclusion Audiovisual presentation in the form of a patient video is a useful tool in the psychological preparation of patients undergoing colorectal surgery.
Microsatellite markers for Hylocomium splendens (Hylocomiaceae)
Authors: Vik Unni , Halvorsen Rune , Ohlson Mikael , Rydgren Knut , Carlsen Tor , Korpelainen Helena , Kauserud Håvard 
Published: August 2012

• Premise of the study: The perennial feather moss Hylocomium splendens is one of the most widely distributed and common bryophytes in the Northern Hemisphere and has, because of its capacity to grow under a wide range of environmental conditions, been used as a biomonitor for atmospheric metal deposition in Europe.• Methods and Results: We present a multiplex approach for the analysis of 14 microsatellite markers tested on 194 H. splendens gametophytes. Ten of the markers are developed recently, and are presented for the first time in this paper, whereas four were previously developed but have not been used for population genetic investigations.• Conclusions: The microsatellite markers reported here will provide a powerful tool for further research on population genetic structure in H. splendens.
The evolutionary potential of Baker's weediness traits in the common morning glory, Ipomoea purpurea (Convolvulaceae)
Authors: Chaney Lindsay , Baucom Regina S. 
Published: August 2012

• Premise of the study: Many reports have cited Baker's list of weediness traits, or those that exemplify the “ideal” weed, yet few have considered the evolutionary potential of such traits as a group. Thus, it is unknown whether constraints on the evolution of increased weediness, such as a lack of genetic variation or genetic correlations between the traits, are present. Ipomoea purpurea, the common morning glory, is a problematic weed that exhibits many of Baker's ideal weed traits.• Methods: We used progeny from a half/full‐sib breeding design in a series of three greenhouse experiments to assess the presence of genetic variation, narrow sense heritabilities, and genetic correlations in Baker's growth, competition, and fitness “weediness” traits in two populations of I. purpurea.• Key results: We uncovered genetic variation underlying reproductive fitness traits and competitive ability in at least one population, but no evidence of genetic variation underlying growth rate in either population. Genetic correlations between many of the weediness characters differed significantly from zero; however, their direction and/or magnitude differed between populations.• Conclusions: We found that increased weediness in the common morning glory is more likely to occur through selection on reproductive output and competitive ability rather than through selection on growth rate. Assessing Baker's traits in a quantitative genetics framework can provide a solid perspective on their evolutionary potential and a unique framework within which to determine how weeds will respond to different environmental stresses and/or scenarios of global climate change.