bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues
Authors: Chen Jia-Shing , Lin Shang-Chi , Chen Chia-Ying , Hsieh Yen-Ting , Pai Ping-Hui , Chen Long-Kung , Lee Shengwan 
Published: January 2014

Abstract

Background
Rice is one of the major crop species in the world helping to sustain approximately half of the global population’s diet especially in Asia. However, due to the impact of extreme climate change and global warming, rice crop production and yields may be adversely affected resulting in a world food crisis. Researchers have been keen to understand the effects of drought, temperature and other environmental stress factors on rice plant growth and development. Gene expression microarray technology represents a key strategy for the identification of genes and their associated expression patterns in response to stress. Here, we report on the development of the rice OneArray® microarray platform which is suitable for two major rice subspecies, japonica and indica.

Results
The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. The results were submitted to NCBI’s Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE50844 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50844). A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes. GO enrichment analysis demonstrates these results are in agreement with the known physiological processes of the different organs/tissues. Furthermore, qRT-PCR validation was performed on 66 genes, and found to significantly correlate with the microarray results (R = 0.95, p < 0.001***).

Conclusion
The rice OneArray® 22 K microarray, the first rice microarray, covering both japonica and indica subspecies was designed and validated in a comprehensive study of gene expression in rice tissues. The rice OneArray® microarray platform revealed high specificity and sensitivity. Additional information for the rice OneArray® microarray can be found at http://www.phalanx.com.tw/index.php.
Antidepressant effects of crocin and its effects on transcript and protein levels of CREB, BDNF, and VGF in rat hippocampus
Authors: Vahdati Hassani Faezeh , Naseri Vahideh , Razavi Bibi Marjan , Mehri Soghra , Abnous Khalil , Hosseinzadeh Hossein 
Published: January 2014

Abstract

Background
Antidepressants have been shown to affect levels of brain-derived neurotrophic factor (BDNF) and VGF (non-acronymic) whose transcriptions are dependent on cAMP response element binding protein (CREB) in long term treatment. The aim of this study was to verify the subacute antidepressant effects of crocin, an active constituent of saffron (Crocus sativus L.), and its effects on CREB, BDNF, and VGF proteins, transcript levels and amount of active, phosphorylated CREB (P-CREB) protein in rat hippocampus.

Methods
Crocin (12.5, 25, and 50 mg/kg), imipramine (10 mg/kg; positive control) and saline (1 mL/kg; neutral control) were administered intraperitoneally (IP) to male Wistar rats for 21 days. The antidepressant effects were studied using the forced swimming test (FST) on day 21 after injection. Protein expression and transcript levels of genes in the rat hippocampus were evaluated using western blot and quantitative reverse transcription-polymerase chain reaction (qRT-PCR), respectively.

Results
Crocin significantly reduced the immobility time in the FST. Western blot analysis showed that 25 and 50 mg/kg of crocin increased the levels of CREB and BDNF significantly and dose dependently. All doses of crocin increased the VGF levels in a dose-dependent manner. Levels of p-CREB increased significantly by 50 mg/kg dose of crocin. Only 12.5 mg/kg crocin could significantly increase the transcript levels of BDNF. No changes in CREB and VGF transcript levels were observed in all groups.

Conclusions
These results suggest that crocin has antidepressant-like action by increasing CREB, BDNF and VGF levels in hippocampus.
What are the non-food impacts of GM crop cultivation on farmers’ health?
Authors: Racovita Monica , Obonyo Dennis Ndolo , Craig Wendy , Ripandelli Decio 
Published: January 2014

Abstract
Background
With a steady increase in the area cultivated with genetically modified (GM) crops, the impacts of GM crop cultivation are coming under closer scrutiny around the world. The impacts on humans usually refer to possible risks to health occurring as a result of the GM food consumption. Other concerns, such as the claims of human health benefits arising from the cultivation of GM crops via reduced use of pesticides could be considered, if at all, under economic impacts of the technology. Similarly, other human health impacts could occur as a result of a modification of the amount of pesticides residues found in underground water, which could be considered under environmental impacts.
Yet many GM crops are not consumed on-farm, either because they require processing before becoming edible (such as soya bean, cottonseed and oilseed) or because the entire harvest is sold to maximise profits. It would be certainly difficult to demonstrate the importance of GM foods health effects versus the non-food health effects of GM crop cultivation on farmers. However, the non-food health effects, although apparently receiving less attention, deserve a closer look because of their potential economic and environmental links.

Methods/design
The primary research question is: What are the non-food impacts of GM crop cultivation on farmers’ health? To address specifically the main research question, the analysis focuses on two related secondary questions: 1) Does the cultivation of GM crops result in a lower number of pesticide-related poisonings? and 2) Does the cultivation of GM crops allow for higher financial resources to be used by farmers to improve their and their family’s health status? Further, the review will also evaluate the extent to which information relevant to the two secondary questions is freely-available. The abstracts of non-free articles, alongside their bibliographic details, will be included in a separate table, and if the information supplied would be detailed enough, a summary will be provided. The search and assessment methodologies (especially the search string, inclusion/exclusion criteria, data extraction table, data synthesis and presentation) were adapted following problems overcome, and experience gained, during a scoping search.
Tertiary structure prediction and identification of druggable pocket in the cancer biomarker – Osteopontin-c
Authors: Sivakumar Subramaniam , Niranjali Devaraj Sivasitambaram 
Published: January 2014

AbstractBackgroundOsteopontin (Eta, secreted sialoprotein 1, opn) is secreted from different cell types including cancer cells. Three splice variant forms namely osteopontin-a, osteopontin-b and osteopontin-c have been identified. The main astonishing feature is that osteopontin-c is found to be elevated in almost all types of cancer cells. This was the vital point to consider it for sequence analysis and structure predictions which provide ample chances for prognostic, therapeutic and preventive cancer research.MethodsOsteopontin-c gene sequence was determined from Breast Cancer sample and was translated to protein sequence. It was then analyzed using various software and web tools for binding pockets, docking and druggability analysis. Due to the lack of homological templates, tertiary structure was predicted using ab-initio method server – I-TASSER and was evaluated after refinement using web tools. Refined structure was compared with known bone sialoprotein electron microscopic structure and docked with CD44 for binding analysis and binding pockets were identified for drug designing.ResultsSignal sequence of about sixteen amino acid residues was identified using signal sequence prediction servers. Due to the absence of known structures of similar proteins, three dimensional structure of osteopontin-c was predicted using I-TASSER server. The predicted structure was refined with the help of SUMMA server and was validated using SAVES server. Molecular dynamic analysis was carried out using GROMACS software. The final model was built and was used for docking with CD44. Druggable pockets were identified using pocket energies.ConclusionsThe tertiary structure of osteopontin-c was predicted successfully using the ab-initio method and the predictions showed that osteopontin-c is of fibrous nature comparable to firbronectin. Docking studies showed the significant similarities of QSAET motif in the interaction of CD44 and osteopontins between the normal and splice variant forms of osteopontins and binding pockets analyses revealed several pockets which paved the way to the identification of a druggable pocket.
Facilitators and barriers of adaptation to diabetes: experiences of Iranian patients
Authors: Karimi Moonaghi Hossein , Namdar Areshtanab Hossein , Jouybari Leila , Arshadi Bostanabad Mohammad , McDonald Heather 
Published: January 2014

Abstract
Background
Diabetes mellitus is one of the most challenging and burdensome chronic diseases of the 21st century and More than 1% of the Iranian urban population older than 20 years develops Type 2 diabetes each year. Living with diabetes mellitus has been described as a dynamic personal transitional adaptation, based on restructuring of the illness perceived experience and management of the self. Adaptation to Type 2 Diabetes mellitus is an integral part of diabetes care.
This study explored the experiences of facilitators and barriers adaptation to Type 2 Diabetes by Iranian patients.

Methods
This study was conducted by using qualitative content analysis. Data were collected via in-depth, semi-structured and face to face interviews with 15 patients with type2 diabetes.

Results
Three themes emerged from collected data, including a) individual context with Beliefs, personal background, and previous experience subthemes. b) supportive system with Family, Society and Health organizations subthemes and c) self-comparison with comparison with other diabetes and comparison with other diseases subthemes.

Conclusions
Identifying and managing Facilitators and Barriers adaptation to Type 2 Diabetes mellitus are an integral part of diabetes care. This study provides a better understanding of the factors from perspective of patients and it can be utilized by health care providers to adapt their health care and education contents to better meet the needs of people with diabetes.
The teleost acute-phase inflammatory response and caspase activation by a novel alarmin-like ligand
Authors: Jaso-Friedmann Liliana , Leary John H , Camus A C , Evans Donald L 
Published: January 2014

ABSTRACTThis study tested the hypothesis that NCAMP-1 has alarmin-like properties and activates the caspase-1-binding site in cells of the teleost bone marrow (equivalent). In mammals, alarmins have been studied extensively; however, in teleosts, little is known about their identity and functions. Similar to alarmins, NCAMP-1 has a broad spectrum of bacteriolytic activity. NCAMP-1 is constitutively present in CF serum, and levels were increased following infection with Edwardsiella ictaluri. Binding to AK cells was determined with rNCAMP-1 and an anti-His-tag antibody. In vitro treatment of AK (bone marrow equivalent) or spleen cells with rNCAMP-1 increased the IL-1β message three- to fivefold at 3 h, 6 h, and 9 h post-treatment. The association of NCAMP-1 with the activities of alarmin ATP and the acute inflammatory response was demonstrated by NCAMP-1-induced P2X7R pore opening and YO-PRO-1 cellular influx. The association of NCAMP-1 binding with inflammasome activation was demonstrated by NCAMP-1 activation of the caspase-1-binding site for tetrapeptide Z-YVAD-FMK. In competition assays, this tetrapeptide competitively inhibited subsequent binding by the pan-caspase substrate tripeptide FAM-VAD-FMK. Lymphocyte-like cells from the spleen were 16%+, and epithelial cells were also positive for NCAMP-1. IHC staining and confocal microscopy confirmed the cytosolic existence of NCAMP-1 in lymphoreticular tissue and IL-1β in AK cells. CF T cell lines G14D and 28S.3 expressed NCAMP-1 in the cytosol and in storage granules. These studies strongly suggested that NCAMP-1 is an alarmin-like ligand with similar but distinct activities to those of ATP and HMGB-1.
Activation of NK cells is associated with HIV-1 disease progression
Authors: Kuri-Cervantes Leticia , de Oca Gonzalo Salgado-Montes , Ávila-Ríos Santiago , Hernández-Juan Ramón , Reyes-Terán Gustavo 
Published: January 2014

ABSTRACTThe main predictor of HIV-1 disease progression is CD8+ T cell activation, characterized by elevated expression of CD38 and HLA-DR. NK cells are also activated in viremic HIV-1-infected individuals. However, the relationship between NK cell activation and HIV-1 disease progression remains undefined. We characterized NK cell activation and its association with disease progression in treatment of naive HIV-1-infected individuals, who naturally maintained low/undetectable viremia (elite and viremic controllers), compared with progressors and AIDS subjects, and treated individuals. Our results show that CD38 expression on NK cells, predominantly in the cytotoxic CD56dimCD16+ subset, is associated with HIV-1 disease progression (CD4+ T cell count and pVL), T cell activation (percentage of CD38+HLA-DR+ T cells), sCD14, inflammation, and innate immune activation. Moreover, NK cell activation is increased in HIV-1-infected subjects progressing to AIDS but not in elite and viremic controllers. ART partially reduces the proportion of activated NK cells. Furthermore, our results show that individuals, who naturally control viremia, maintain low levels of innate immune activation similar to those of uninfected controls.
Ovarian Surface Epithelium: Biology, Endocrinology, and Pathology*
Authors: Auersperg Nelly , Wong Alice S. T. , Choi Kyung-Chul , Kang Sung Keun , Leung Peter C. K. 
Published: January 2014

AbstractThe epithelial ovarian carcinomas, which make up more than 85% of human ovarian cancer, arise in the ovarian surface epithelium (OSE). The etiology and early events in the progression of these carcinomas are among the least understood of all major human malignancies because there are no appropriate animal models, and because methods to culture OSE have become available only recently. The objective of this article is to review the cellular and molecular mechanisms that underlie the control of normal and neoplastic OSE cell growth, differentiation, and expression of indicators of neoplastic progression. We begin with a brief discussion of the development of OSE, from embryonic to the adult. The pathological and genetic changes of OSE during neoplastic progression are next summarized. The histological characteristics of OSE cells in culture are also described. Finally, the potential involvement of hormones, growth factors, and cytokines is discussed in terms of their contribution to our understanding of the physiology of normal OSE and ovarian cancer development.
Recombinant DNA Technology in the Treatment of Diabetes: Insulin Analogs
Authors: Vajo Zoltan , Fawcett Janet , Duckworth William C. 
Published: January 2014

AbstractAfter more than half a century of treating diabetics with animal insulins, recombinant DNA technologies and advanced protein chemistry made human insulin preparations available in the early 1980s. As the next step, over the last decade, insulin analogs were constructed by changing the structure of the native protein with the goal of improving the therapeutic properties of it, because the pharmacokinetic characteristics of rapid-, intermediate-, and long-acting preparations of human insulin make it almost impossible to achieve sustained normoglycemia. The first clinically available insulin analog, lispro, confirmed the hopes by showing that improved glycemic control can be achieved without an increase in hypoglycemic events. Two new insulin analogs, insulin glargine and insulin aspart, have recently been approved for clinical use in the United States, and several other analogs are being intensively tested. Thus, it appears that a rapid acceleration of basic and clinical research in this arena will be seen, which will have direct significance to both patients and their physicians. The introduction of new short-acting analogs and the development of the first truly long-acting analogs and the development of analogs with increased stability, less variability, and perhaps selective action, will help to develop more individualized treatment strategies targeted to specific patient characteristics and to achieve further improvements in glycemic control. Data on the currently available and tested analogs, as well as data on those currently being developed, are reviewed.
Peptide YY (PYY) Gene Polymorphisms in the 3′-Untranslated Region and Proximal Promoter Regions Regulate Cellular Gene Expression and PYY Secretion and Metabolic Syndrome Traits in Vivo
Authors: Shih Pei-an Betty , Wang Lei , Chiron Stephane , Wen Gen , Nievergelt Caroline , Mahata Manjula , Khandrika Srikrishna , Rao Fangwen , Fung Maple M. , Mahata Sushil K. , Hamilton Bruce A. , O'Connor Daniel T. 
Published: January 2014

Abstract

Rationale
Obesity is a heritable trait that contributes to hypertension and subsequent cardiorenal disease risk; thus, the investigation of genetic variation that predisposes individuals to obesity is an important goal. Circulating peptide YY (PYY) is known for its appetite and energy expenditure-regulating properties; linkage and association studies have suggested that PYY genetic variation contributes to susceptibility for obesity, rendering PYY an attractive candidate for study of disease risk.

Design
To explore whether common genetic variation at the human PYY locus influences plasma PYY or metabolic traits, we systematically resequenced the gene for polymorphism discovery and then genotyped common single-nucleotide polymorphisms across the locus in an extensively phenotyped twin sample to determine associations. Finally, we experimentally validated the marker-on-trait associations using PYY 3′-untranslated region (UTR)/reporter and promoter/reporter analyses in neuroendocrine cells.

Results
Four common genetic variants were discovered across the locus, and three were typed in phenotyped twins. Plasma PYY was highly heritable (P &lt; 0.0001), and genetic pleiotropy was noted between plasma PYY and body mass index (BMI) (P = 0.03). A PYY haplotype extending from the proximal promoter (A-23G, rs2070592) to the 3′-UTR (C+1134A, rs162431) predicted not only plasma PYY (P = 0.009) but also other metabolic syndrome traits. Functional studies with transfected luciferase reporters confirmed regulatory roles in altering gene expression for both 3′-UTR C+1134A (P &lt; 0.001) and promoter A-23G (P = 0.0016).

Conclusions
Functional genetic variation at the PYY locus influences multiple heritable metabolic syndrome traits, likely conferring susceptibility to obesity and subsequent cardiorenal disease.
Positive and Negative Regulation of the Rat Vasopressin Gene Promoter*
Authors: Iwasaki Yasumasa , Oiso Yutaka , Saito Hidehiko , Majzoub Joseph A. 
Published: January 2014

AbstractTo study the transcriptional regulation of the vasopressin gene in vitro, 3 kb of the 5′ regulatory region of the rat vasopressin gene was isolated and subcloned, along with a series of various deletion mutants, into vectors containing the luciferase reporter gene. After transfecting these genes transiently into the human choriocarcinoma cell line JEG-3 along with a glucocorticoid receptor (GR) expression vector, transcriptional activity was quantitated using the luciferase assay. Forskolin, 8-bromo-cAMP, and protein kinase A catalytic subunit expression all markedly increased transcription from the 3-kb promoter. Analyses with deletion mutants of the promoter showed that two cAMP-responsive element (CRE)-like sequences (−227 to −220 bp and −123 to −116 bp) contribute to this positive regulation. Expression of KCREB, a dominant negative mutant of the cAMP-responsive element binding protein (CREB), suggested the involvement of CREB. Transfection of the activator protein 2 (AP2) DNA consensus sequence partially blocked transcription. Dexamethasone suppressed forskolin-stimulated expression. The negative effect of glucocorticoid was GR dependent and may be mediated by a mechanism not involving GR binding to DNA because it was independent of the putative glucocorticoid-responsive element previously reported in the vasopressin promoter (−622 to −608 bp) and was preserved in the shorter promoter constructs in which no glucocorticoid-responsive element-like sequence was found. Our data suggest that several trans-acting factors including CREB, AP2, and GR are likely to be involved in vasopressin gene transcription and that the positive and negative regulation of vasopressin gene transcription is complex.