bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mumesieb. et zucc.)
Authors: Sun Lidan , Zhang Qixiang , Xu Zongda , Yang Weiru , Guo Yu , Lu Jiuxing , Pan Huitang , Cheng Tangren , Cai Ming 
Published: October 2013

Abstract

Background
Mei (Prunus mume Sieb. et Zucc.) is a famous ornamental plant and fruit crop grown in East Asian countries. Limited genetic resources, especially molecular markers, have hindered the progress of mei breeding projects. Here, we performed low-depth whole-genome sequencing of Prunus mume ‘Fenban’ and Prunus mume ‘Kouzi Yudie’ to identify high-quality polymorphic markers between the two cultivars on a large scale.

Results
A total of 1464.1 Mb and 1422.1 Mb of ‘Fenban’ and ‘Kouzi Yudie’ sequencing data were uniquely mapped to the mei reference genome with about 6-fold coverage, respectively. We detected a large number of putative polymorphic markers from the 196.9 Mb of sequencing data shared by the two cultivars, which together contained 200,627 SNPs, 4,900 InDels, and 7,063 SSRs. Among these markers, 38,773 SNPs, 174 InDels, and 418 SSRs were distributed in the 22.4 Mb CDS region, and 63.0% of these marker-containing CDS sequences were assigned to GO terms. Subsequently, 670 selected SNPs were validated using an Agilent’s SureSelect solution phase hybridization assay. A subset of 599 SNPs was used to assess the genetic similarity of a panel of mei germplasm samples and a plum (P. salicina) cultivar, producing a set of informative diversity data. We also analyzed the frequency and distribution of detected InDels and SSRs in mei genome and validated their usefulness as DNA markers. These markers were successfully amplified in the cultivars and in their segregating progeny.

Conclusions
A large set of high-quality polymorphic SNPs, InDels, and SSRs were identified in parallel between ‘Fenban’ and ‘Kouzi Yudie’ using low-depth whole-genome sequencing. The study presents extensive data on these polymorphic markers, which can be useful for constructing high-resolution genetic maps, performing genome-wide association studies, and designing genomic selection strategies in mei.
Genome-wide association study on serum alkaline phosphatase levels in a Chinese population
Authors: Li Jun , Gui Lixuan , Wu Chen , He Yunfeng , Zhou Li , Guo Huan , Yuan Jing , Yang Binyao , Dai Xiayun , Deng Qifei , Huang Suli , Guan Lei , Hu Die , Deng Siyun , Wang Tian , Zhu Jiang , Min Xinwen , Lang Mingjian , Li Dongfeng , Yang Handong , Hu Frank B , Lin Dongxin , Wu Tangchun , He Meian 
Published: October 2013

AbstractBackgroundSerum alkaline phosphatase (ALP) is a complex phenotype influenced by both genetic and environmental factors. Recent Genome-Wide Association Studies (GWAS) have identified several loci affecting ALP levels; however, such studies in Chinese populations are limited. We performed a GWAS analyzing the association between 658,288 autosomal SNPs and serum ALP in 1,461 subjects, and replicated the top SNPs in an additional 8,830 healthy Chinese Han individuals. The interactions between significant locus and environmental factors on serum ALP levels were further investigated.ResultsThe association betweenABOlocus and serum ALP levels was replicated (P = 2.50 × 10-21, 1.12 × 10-56and 2.82 × 10-27for SNP rs8176720, rs651007 and rs7025162 onABOlocus, respectively). SNP rs651007 accounted for 2.15% of the total variance of serum ALP levels independently of the other 2 SNPs. When comparing our findings with previously published studies, ethnic differences were observed across populations. A significant interaction betweenABOrs651007 and overweight and obesity was observed (FDRfor interaction was 0.036); for individuals with GG genotype, those with normal weight and those who were overweight or obese have similar serum ALP concentrations; minor allele A of rs651007 remarkably reduced serum ALP levels, but this effect was attenuated in overweight and obese individuals.ConclusionsOur findings indicate thatABOlocus is a major determinant for serum ALP levels in Chinese Han population. Overweight and obesity modifies the effect ofABOlocus on serum ALP concentrations.
DNMT1 and AIM1 Imprinting in human placenta revealed through a genome-wide screen for allele-specific DNA methylation
Authors: Das Radhika , Lee Yew Kok , Strogantsev Ruslan , Jin Shengnan , Lim Yen Ching , Ng Poh Yong , Lin Xueqin Michelle , Chng Keefe , Yeo George SH , Ferguson-Smith Anne C , Ding Chunming 
Published: October 2013

Abstract

Background
Genomic imprinting is an epigenetically regulated process wherein genes are expressed in a parent-of-origin specific manner. Many imprinted genes were initially identified in mice; some of these were subsequently shown not to be imprinted in humans. Such discrepancy reflects developmental, morphological and physiological differences between mouse and human tissues. This is particularly relevant for the placenta. Study of genomic imprinting thus needs to be carried out in a species and developmental stage-specific manner. We describe here a new strategy to study allele-specific DNA methylation in the human placenta for the discovery of novel imprinted genes.

Results
Using this methodology, we confirmed 16 differentially methylated regions (DMRs) associated with known imprinted genes. We chose 28 genomic regions for further testing and identified two imprinted genes (DNMT1 and AIM1). Both genes showed maternal allele-specific methylation and paternal allele-specific transcription. Imprinted expression for AIM1 was conserved in the cynomolgus macaque placenta, but not in other macaque tissues or in the mouse.

Conclusions
Our study indicates that while there are many genomic regions with allele-specific methylation in tissues like the placenta, only a small sub-set of them are associated with allele-specific transcription, suggesting alternative functions for such genomic regions. Nonetheless, novel tissue-specific imprinted genes remain to be discovered in humans. Their identification may help us better understand embryonic and fetal development.
Sec-mediated secretion by Coxiella burnetii
Authors: Stead Christopher M , Omsland Anders , Beare Paul A , Sandoz Kelsi M , Heinzen Robert A 
Published: October 2013

Abstract

Background

Coxiella burnetii is a Gram-negative intracellular bacterial pathogen that replicates within a phagolysosome-like parasitophorous vacuole (PV) of macrophages. PV formation requires delivery of effector proteins directly into the host cell cytoplasm by a type IVB secretion system. However, additional secretion systems are likely responsible for modification of the PV lumen microenvironment that promote pathogen replication.

Results
To assess the potential of C. burnetii to secrete proteins into the PV, we analyzed the protein content of modified acidified citrate cysteine medium for the presence of C. burnetii proteins following axenic (host cell-free) growth. Mass spectrometry generated a list of 105 C. burnetii proteins that could be secreted. Based on bioinformatic analysis, 55 proteins were selected for further study by expressing them in C. burnetii with a C-terminal 3xFLAG-tag. Secretion of 27 proteins by C. burnetii transformants was confirmed by immunoblotting culture supernatants. Tagged proteins expressed by C. burnetii transformants were also found in the soluble fraction of infected Vero cells, indicating secretion occurs ex vivo. All secreted proteins contained a signal sequence, and deletion of this sequence from selected proteins abolished secretion. These data indicate protein secretion initially requires translocation across the inner-membrane into the periplasm via the activity of the Sec translocase.

Conclusions

C. burnetii secretes multiple proteins, in vitro and ex vivo, in a Sec-dependent manner. Possible roles for secreted proteins and secretion mechanisms are discussed.
Lipoproteins of slow-growing Mycobacteria carry three fatty acids and are N-acylated by Apolipoprotein N-Acyltransferase BCG_2070c
Authors: Brülle Juliane K , Tschumi Andreas , Sander Peter 
Published: October 2013

Abstract

Background
Lipoproteins are virulence factors of Mycobacterium tuberculosis. Bacterial lipoproteins are modified by the consecutive action of preprolipoprotein diacylglyceryl transferase (Lgt), prolipoprotein signal peptidase (LspA) and apolipoprotein N- acyltransferase (Lnt) leading to the formation of mature triacylated lipoproteins. Lnt homologues are found in Gram-negative and high GC-rich Gram-positive, but not in low GC-rich Gram-positive bacteria, although N-acylation is observed. In fast-growing Mycobacterium smegmatis, the molecular structure of the lipid modification of lipoproteins was resolved recently as a diacylglyceryl residue carrying ester-bound palmitic acid and ester-bound tuberculostearic acid and an additional amide-bound palmitic acid.

Results
We exploit the vaccine strain Mycobacterium bovis BCG as model organism to investigate lipoprotein modifications in slow-growing mycobacteria. Using Escherichia coli Lnt as a query in BLASTp search, we identified BCG_2070c and BCG_2279c as putative lnt genes in M. bovis BCG. Lipoproteins LprF, LpqH, LpqL and LppX were expressed in M. bovis BCG and BCG_2070c lnt knock-out mutant and lipid modifications were analyzed at molecular level by matrix-assisted laser desorption ionization time-of-flight/time-of-flight analysis. Lipoprotein N-acylation was observed in wildtype but not in BCG_2070c mutants. Lipoprotein N- acylation with palmitoyl and tuberculostearyl residues was observed.

Conclusions
Lipoproteins are triacylated in slow-growing mycobacteria. BCG_2070c encodes a functional Lnt in M. bovis BCG. We identified mycobacteria-specific tuberculostearic acid as further substrate for N-acylation in slow-growing mycobacteria.
Transcriptome analysis of heat stress response in switchgrass (Panicum virgatumL.)
Authors: Li Yong-Fang , Wang Yixing , Tang Yuhong , Kakani Vijaya Gopal , Mahalingam Ramamurthy 
Published: October 2013

AbstractBackgroundGlobal warming predictions indicate that temperatures will increase by another 2-6°C by the end of this century. High temperature is a major abiotic stress limiting plant growth and productivity in many areas of the world. Switchgrass (Panicum virgatumL.) is a model herbaceous bioenergy crop, due to its rapid growth rate, reliable biomass yield, minimal requirements of water and nutrients, adaptability to grow on marginal lands and widespread distribution throughout North America. The effect of high temperature on switchgrass physiology, cell wall composition and biomass yields has been reported. However, there is void in the knowledge of the molecular responses to heat stress in switchgrass.ResultsWe conducted long-term heat stress treatment (38°/30°C, day/night, for 50 days) in the switchgrass cultivar Alamo. A significant decrease in the plant height and total biomass was evident in the heat stressed plants compared to controls. Total RNA from control and heat stress samples were used for transcriptome analysis with switchgrass Affymetrix genechips. Following normalization and pre-processing, 5365 probesets were identified as differentially expressed using a 2-fold cutoff. Of these, 2233 probesets (2000 switchgrass unigenes) were up-regulated, and 3132 probesets (2809 unigenes) were down-regulated. Differential expression of 42 randomly selected genes from this list was validated using RT-PCR. Rice orthologs were retrieved for 78.7% of the heat stress responsive switchgrass probesets. Gene ontology (GOs) enrichment analysis using AgriGO program showed that genes related to ATPase regulator, chaperone binding, and protein folding was significantly up-regulated. GOs associated with protein modification, transcription, phosphorus and nitrogen metabolic processes, were significantly down-regulated by heat stress.ConclusionsPlausible connections were identified between the identified GOs, physiological responses and heat response phenotype observed in switchgrass plants. Comparative transcriptome analysis in response to heat stress among four monocots – switchgrass, rice, wheat and maize identified 16 common genes, most of which were associated with protein refolding processes. These core genes will be valuable biomarkers for identifying heat sensitive plant germplasm since they are responsive to both short duration as well as chronic heat stress treatments, and are also expressed in different plant growth stages and tissue types.
Herpes zoster surveillance using electronic databases in the Valencian Community (Spain)
Authors: Morant-Talamante Nuria , Diez-Domingo Javier , Martínez-Úbeda Sergio , Puig-Barberá Joan , Alemán-Sánchez Sara , Pérez-Breva Lina 
Published: October 2013

Abstract

Background
Epidemiologic data of Herpes Zoster (HZ) disease in Spain are scarce. The objective of this study was to assess the epidemiology of HZ in the Valencian Community (Spain), using outpatient and hospital electronic health databases.

Methods
Data from 2007 to 2010 was collected from computerized health databases of a population of around 5 million inhabitants. Diagnoses were recorded by physicians using the International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM). A sample of medical records under different criteria was reviewed by a general practitioner, to assess the reliability of codification.

Results
The average annual incidence of HZ was 4.60 per 1000 persons-year (PY) for all ages (95% CI: 4.57-4.63), is more frequent in women [5.32/1000PY (95% CI: 5.28-5.37)] and is strongly age-related, with a peak incidence at 70-79 years. A total of 7.16/1000 cases of HZ required hospitalization.

Conclusions
Electronic health database used in the Valencian Community is a reliable electronic surveillance tool for HZ disease and will be useful to define trends in disease burden before and after HZ vaccine introduction.
Clinical and laboratory characteristics of penicilliosis marneffei among patients with and without HIV infection in Northern Thailand: a retrospective study
Authors: Kawila Rathakarn , Chaiwarith Romanee , Supparatpinyo Khuanchai 
Published: October 2013

Abstract

Background
Penicilliosis marneffei is increasingly observed in individuals without HIV infection. This study aimed to compare the clinical and laboratory features among HIV infected and uninfected individuals with penicilliosis marneffei.

Methods
A retrospective cohort study was conducted between January 1, 2007 and December 31, 2011 at Chiang Mai University Hospital. We included individuals who were ≥15 years of age and presented with culture-proven P. marneffei infection.

Results
116 HIV-infected and 34 HIV-uninfected patients were enrolled. Comparing to HIV-infected patients, HIV-uninfected patients were older; less likely to have fever, splenomegaly, and umbilicated skin lesions; more likely to have Sweet’s syndrome and bone and joint infections; had higher white blood cell count, platelet count, and CD4 cell count; had lower alanine transaminase (ALT); and less likely to have positive fungal blood cultures. The mortality rates were 20.7% and 29.4% among HIV infected and uninfected patients, respectively.

Conclusions
Clinical manifestations of penicilliosis marneffei are different between patients with and without HIV infection. Physician’s awareness of this disease in HIV-uninfected patients may prompt the diagnosis and timely treatment, and can lead to a better outcome.
Effects of vitamin D receptor polymorphisms on urolithiasis risk: a meta-analysis
Authors: Zhang Pan , Nie Wei , Jiang Hong 
Published: October 2013

AbstractBackgroundSeveral studies analyzed the associations ofVitamin D receptor(VDR) polymorphisms with urolithiasis risk in different ethnic groups. However, the results were inconclusive. To evaluate a more precise estimation of the relationship, a meta-analysis was performed.MethodsPubmed, EMBASE, Wanfang Database, China National Knowledge Infrastructure (CNKI) and Weipu Database were searched. Data were extracted independently by two investigators. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of associations.ResultsTwenty-three case–control studies were included in this meta-analysis. Significant associations betweenApaI,BsmI,FokI, andTaqIpolymorphisms and urolithiasis risk were observed. However, sensitivity analyses forBsmIandFokIpolymorphisms indicated that the results were not reliable and credible. In addition, there was a significant association of theApaI-TaqIhaplotype with urolithiasis risk.ConclusionsThis meta-analysis suggested thatApaIandTaqIpolymorphisms inVDRgene were associated with urolithiasis risk.
Impaired endocytosis in proximal tubule from subchronic exposure to cadmium involves angiotensin II type 1 and cubilin receptors
Authors: Santoyo-Sánchez Mitzi Paola , Pedraza-Chaverri José , Molina-Jijón Eduardo , Arreola-Mendoza Laura , Rodríguez-Muñoz Rafael , Barbier Olivier Christophe 
Published: October 2013

AbstractBackgroundChronic exposure to low cadmium (Cd) levels produces urinary excretion of low molecular weight proteins, which is considered the critical effect of Cd exposure. However, the mechanisms involved in Cd-induced proteinuria are not entirely clear. Therefore, the present study was designed to evaluate the possible role of megalin and cubilin (important endocytic receptors in proximal tubule cells) and angiotensin II type 1 (AT1) receptor on Cd-induced microalbuminuria.MethodsFour groups of female Wistar rats were studied. Control (CT) group, vehicle-treated rats; LOS group, rats treated with losartan (an AT1 antagonist) from weeks 5 to 8 (10 mg/kg/day by gavage); Cd group, rats subchronically exposed to Cd (3 mg/kg/day by gavage) during 8 weeks, and Cd + LOS group, rats treated with Cd for 8 weeks and LOS from weeks 5–8. Kidney Cd content, glomerular function (evaluated by creatinine clearance and plasma creatinine), kidney injury and tubular function (evaluated by Kim-1 expression, urinary excretion of N-acetyl-β-D-glucosaminidase (NAG) and glucose, and microalbuminuria), oxidative stress (measured by lipid peroxidation and NAD(P)H oxidase activity), mRNA levels of megalin, expressions of megalin and cubilin (by confocal microscopy) and AT1 receptor (by Western blot), were measured in the different experimental groups. Data were analyzed by one-way ANOVA or Kruskal-Wallis test using GraphPad Prism 5 software (Version 5.00). P < 0.05 was considered statistically significant.ResultsAdministration of Cd (Cd and Cd + LOS groups) increased renal Cd content. LOS-treatment decreased Cd-induced microalbuminuria without changes in: plasma creatinine, creatinine clearance, urinary NAG and glucose, oxidative stress, mRNA levels of megalin and cubilin, neither protein expression of megalin nor AT1 receptor, in the different experimental groups studied. However, Cd exposure did induce the expression of the tubular injury marker Kim-1 and decreased cubilin protein levels in proximal tubule cells whereas LOS-treatment restored cubilin levels and suppressed Kim-1 expression.ConclusionLOS treatment decreased microalbuminuria induced by Cd apparently through a cubilin receptor-dependent mechanism but independent of megalin.
Estimation of 10 - year probability bone fracture in a selected sample of Palestinian people using fracture risk assessment tool
Authors: Aker Mai B , Taha Adham S Abu , Zyoud Sa’ed H , Sawalha Ansam F , Al-Jabi Samah W , Sweileh Waleed M 
Published: October 2013

Abstract

Background
The Fracture Risk Assessment (FRAX) tool has been developed by the World Health Organization (WHO) to calculate 10-year probability hip fracture (HP) or major osteoporotic fracture (MOF). The objective of this study was to assess the 10-year probability of MOF and HF among a selected sample of Palestinian people.

Methods
A sample of 100 subjects was studied. Dual energy X-ray absorpitometry was performed to measure bone mineral density (BMD) which was then inserted into FRAX Palestine online WHO tool to calculate the 10-year probability of MOF and HF.

Results
The median age of participants was 61.5 years and the majority (79%) were females. The median (interquartile range) of femoral hip BMD was 0.82 (0.76-0.92) g/cm2. The mean vertebral and hip T scores were -1.41 ± 0.13 SDs and -0.91 ± 0.10 SDs respectively. About one fifth of the sample (21%) had vertebral osteoporosis and 5% had hip osteoporosis. The median (interquartile range) 10-year probability of MOF and HF based on BMD were 3.7 (2.43-6.18)%, and 0.30 (0.10-0.68)% respectively.

Conclusion
Osteoporosis is common among Palestinian people above 50 years old. Bone fracture prevention strategies and research should be a priority in Palestine. Using FRAX might be a helpful screening tool in primary healthcare centres in Palestine.
Secretory expression of biologically active human Herpes virus interleukin-10 analogues in Escherichia colivia a modified Sec-dependent transporter construct
Authors: Förster Sarah , Brandt Manuela , Mottok Dorothea S , Zschüttig Anke , Zimmermann Kurt , Blattner Frederick R , Gunzer Florian , Pöhlmann Christoph 
Published: October 2013

Abstract

Background
Interleukin-10 homologues encoded by Herpes viruses such as Epstein-Barr virus (EBV) and human cytomegalovirus (HCMV) hold interesting structural and biological characteristics compared to human interleukin-10 (hIL-10) that render these proteins promising candidates for therapeutic application in inflammatory bowel disease (IBD). Intestinal delivery of cytokines using bacterial carriers as chassis represents a novel approach for treatment of IBD patients. For proof of concept, a Sec-dependent transporter construct was designed for secretory expression of recombinant viral IL-10 proteins in the periplasm of Escherichia coli laboratory strain BL21 (DE3), which might serve as part of a prospective lysis based delivery and containment system.

Results
The signal peptide of E. coli outer membrane protein F fused to the mature form of the viral IL-10 proteins enabled successful transport into the periplasm, a compartment which seems crucial for proper assembly of the dimeric configuration of the cytokines. Cytokine concentrations in different bacterial compartments were determined by ELISA and achieved yields of 67.8 ng/ml ± 24.9 ng/ml for HCMV IL-10 and 1.5 μg/ml ± 841.4 ng/ml for EBV IL-10 in the periplasm. Immunoblot analysis was used to confirm the correct size of the E. coli-derived recombinant cytokines. Phosphorylation of signal transducer and activator of transcription 3 (STAT3) as part of the signal transduction cascade after IL-10 receptor interaction, as well as suppression of tumor necrosis factor α (TNF-α) release of lipopolysaccharide-stimulated mouse macrophages were used as read-out assays for proving in vitro biological activity of the E. coli derived, recombinant viral IL-10 counterparts.

Conclusions
In this study, proof of principle is provided that E. coli cells are a suitable chassis for secretory expression of viral IL-10 cytokines encoded by codon-optimized synthetic genes fused to the E. coli ompF signal sequence. In vitro biological activity evidenced by activation of transcription factor STAT3 and suppression of TNF-α in mammalian cell lines was shown to be strictly dependent on export of viral IL-10 proteins into the periplasmic compartment. E. coli might serve as carrier system for in situ delivery of therapeutic molecules in the gut, thus representing a further step in the development of novel approaches for treatment of IBD.