bluuebunny/crossref_metadata_2025_split huggingface dataset:
Irf8 regulates macrophage versus neutrophil fate during zebrafish primitive myelopoiesis
Authors: Li Li , Jin Hao , Xu Jin , Shi Yuqian , Wen Zilong 
Published: November 2010

AbstractIn vertebrates, myeloid cells comprise polymorphonuclear and mononuclear lineages that arise from 2 successive waves of development: a transitory primitive wave giving rise to limited myeloid cells during embryonic stage and a definitive wave capable of producing myeloid cells throughout the fetal and adult life. One key unresolved question is what factors dictate polymorphonuclear versus mononuclear lineage fates during myelopoiesis. Here we show that during zebrafish embryogenesis interferon regulatory factor-8 (irf8) is expressed specifically in macrophages but not neutrophils. Suppression of Irf8 function in zebrafish causes a depletion of macrophages and an enhanced output of neutrophils but does not affect the overall number, proliferation, and survival of primitive myeloid cells. These data indicate that the skewed myeloid lineage development in Irf8 knockdown embryos results from a cell-fate switching. Such a conclusion is further supported by the observation showing that overexpression of Irf8 promotes macrophage formation at the expense of neutrophil development. Genetic epistasis analysis reveals that Irf8 acts downstream of Pu.1 but is insufficient to promote macrophage development in the absence of Pu.1. Our findings demonstrate that Irf8 is a critical determinant for neutrophil versus macrophage fate choice during zebrafish primitive myelopoiesis.
Hematogones: a new prognostic factor for acute myeloblastic leukemia
Authors: Chantepie Sylvain P. , Salaün Véronique , Parienti Jean-Jacques , Truquet Florence , Macro Margaret , Cheze Stephane , Vilque Jean Pierre , Reman Oumedaly 
Published: November 2010

Abstract
Acute myeloid leukemia (AML) patient outcomes remain heterogeneous, and new prognostic tools are needed to assess the risk of relapse. Hematogones (HGs) are normal B-lymphocyte precursors, which increase in number in hematologic diseases. The prognostic impact of the presence of detectable HGs on the leukemia-free survival (LFS) and overall survival of 120 consecutive patients with AML in first complete remission was investigated by flow cytometry. Patients who had HG levels more than 0.01% had a significantly better median LFS (29.2 vs 11.7 months; P = .001) and overall survival (not reached vs 23.5 months; P = .011). According to Cox analysis, an HG level more than 0.01% was an independent predictor of LFS (hazard ratio = 0.5; 95% confidence interval, 0.28-0.90, P < .03) when age, leukocytosis, the number of chemotherapy cycles, and the standardized cytogenetic and molecular risk subgroups were controlled for. These results indicate that HG analysis may help to define the risk of relapse in AML patients.
Identification of an Ire1alpha endonuclease specific inhibitor with cytotoxic activity against human multiple myeloma
Authors: Papandreou Ioanna , Denko Nicholas C. , Olson Michael , Van Melckebeke Heleen , Lust Sofie , Tam Arvin , Solow-Cordero David E. , Bouley Donna M. , Offner Fritz , Niwa Maho , Koong Albert C. 
Published: November 2010

Abstract
Activation of the adaptive Ire1-XBP1 pathway has been identified in many solid tumors and hematologic malignancies, including multiple myeloma (MM). Here, we report the identification of STF-083010, a novel small-molecule inhibitor of Ire1. STF-083010 inhibited Ire1 endonuclease activity, without affecting its kinase activity, after endoplasmic reticulum stress both in vitro and in vivo. Treatment with STF-083010 showed significant antimyeloma activity in model human MM xenografts. Similarly, STF-083010 was preferentially toxic to freshly isolated human CD138+ MM cells compared with other similarly isolated cell populations. The identification of this novel Ire1 inhibitor supports the hypothesis that the Ire1-XBP1 axis is a promising target for anticancer therapy, especially in the context of MM.
Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)
Authors: Soler Lucile , Conte Matthew A , Katagiri Takayuki , Howe Aimee E , Lee Bo-Young , Amemiya Chris , Stuart Andrew , Dossat Carole , Poulain Julie , Johnson Jeremy , Di Palma Federica , Lindblad-Toh Kerstin , Baroiller Jean-Francois , D'Cotta Helena , Ozouf-Costaz Catherine , Kocher Thomas D 
Published: November 2010

AbstractBackgroundThe Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species.ResultsWe obtained sequence from one or both ends of 106,259 tilapia BACs. BLAST analysis against the genome assemblies of stickleback, medaka and pufferfish allowed identification of homologies for approximately 25,000 BACs for each species. We calculate that rearrangement breakpoints between tilapia and these species occur about every 3 Mb across the genome. Analysis of 35,000 clones previously assembled into contigs by restriction fingerprints allowed identification of longer-range syntenies.ConclusionsOur data suggest that chromosomal evolution in recent teleosts is dominated by alternate loss of gene duplicates, and by intra-chromosomal rearrangements (~one per million years). These physical maps are a useful resource for comparative positional cloning of traits in cichlid fishes. The paired BAC end sequences from these clones will be an important resource for scaffolding forthcoming shotgun sequence assemblies of the tilapia genome.
Rapid induction of IgE responses to a worm cysteine protease during murine pre-patent schistosome infection
Authors: de Oliveira Fraga Lucia A , Lamb Erika W , Moreno Elizabeth C , Chatterjee Mitali , Dvořák Jan , Delcroix Melaine , Sajid Mohammed , Caffrey Conor R , Davies Stephen J 
Published: November 2010

AbstractBackgroundDuring the pre-patent stage of infection, juvenileSchistosomablood flukes co-opt signals from the adaptive immune system to facilitate parasite development, but the types of responses that are induced at this early stage of infection, and the parasite antigens they target, have not been characterized.ResultsThrough analysis of experimental pre-patent infections, we show that theS. mansonicysteine protease SmCB1 is rapidly targeted by an antigen-specific IgE response. The induction of this response is independent of schistosome eggs as infection with male or female worms alone also induced SmCB1-specific IgE. We also show that the SmCB1-specific IgE response is dependent on cognate CD4+T cell help and IL-4, suggesting that pre-patent Th2 responses provide T cell help for the SmCB1-specific IgE response. Finally, exposed human subjects also produced IgE against SmCB1.ConclusionsOur data demonstrate that, like eggs, schistosome worms also induce functional type 2 responses and that a parasite cysteine protease is an inducer of type 2 responses during the early stages of schistosome infection.
A secreted serine protease of Paracoccidioides brasiliensis and its interactions with fungal proteins
Authors: Parente Juliana A , Salem-Izacc Sílvia M , Santana Jaime M , Pereira Maristela , Borges Clayton L , Bailão Alexandre M , Soares Célia MA 
Published: November 2010

Abstract

Background

Paracoccidioides brasiliensis is a thermodimorphic fungus, the causative agent of paracoccidioidomycosis (PCM). Serine proteases are widely distributed and this class of peptidase has been related to pathogenesis and nitrogen starvation in pathogenic fungi.

Results
A cDNA (Pb sp) encoding a secreted serine protease (Pb SP), was isolated from a cDNA library constructed with RNAs of fungal yeast cells recovered from liver of infected mice. Recombinant Pb SP was produced in Escherichia coli, and used to develop polyclonal antibodies that were able to detect a 66 kDa protein in the P. brasiliensis proteome. In vitro deglycosylation assays with endoglycosidase H demonstrated that Pb SP is a N-glycosylated molecule. The Pb sp transcript and the protein were induced during nitrogen starvation. The Pb sp transcript was also induced in yeast cells infecting murine macrophages. Interactions of Pb SP with P. brasiliensis proteins were evaluated by two-hybrid assay in the yeast Saccharomyces cerevisiae. Pb SP interacts with a peptidyl prolyl cis-trans isomerase, calnexin, HSP70 and a cell wall protein PWP2.

Conclusions
A secreted subtilisin induced during nitrogen starvation was characterized indicating the possible role of this protein in the nitrogen acquisition. Pb SP interactions with other P. brasiliensis proteins were reported. Proteins interacting with Pb SP are related to folding process, protein trafficking and cytoskeleton reorganization.
Functional analysis of the Theobroma cacao NPR1 gene in arabidopsis
Authors: Shi Zi , Maximova Siela N , Liu Yi , Verica Joseph , Guiltinan Mark J 
Published: November 2010

Abstract

Background
The Arabidopsis thaliana NPR1 gene encodes a transcription coactivator (NPR1) that plays a major role in the mechanisms regulating plant defense response. After pathogen infection and in response to salicylic acid (SA) accumulation, NPR1 translocates from the cytoplasm into the nucleus where it interacts with other transcription factors resulting in increased expression of over 2000 plant defense genes contributing to a pathogen resistance response.

Results
A putative Theobroma cacao NPR1 cDNA was isolated by RT-PCR using degenerate primers based on homologous sequences from Brassica, Arabidopsis and Carica papaya. The cDNA was used to isolate a genomic clone from Theobroma cacao containing a putative TcNPR1 gene. DNA sequencing revealed the presence of a 4.5 kb coding region containing three introns and encoding a polypeptide of 591 amino acids. The predicted TcNPR1 protein shares 55% identity and 78% similarity to Arabidopsis NPR1, and contains each of the highly conserved functional domains indicative of this class of transcription factors (BTB/POZ and ankyrin repeat protein-protein interaction domains and a nuclear localization sequence (NLS)). To functionally define the TcNPR1 gene, we transferred TcNPR1 into an Arabidopsis npr1 mutant that is highly susceptible to infection by the plant pathogen Pseudomonas syringae pv. tomato DC3000. Driven by the constitutive CaMV35S promoter, the cacao TcNPR1 gene partially complemented the npr1 mutation in transgenic Arabidopsis plants, resulting in 100 fold less bacterial growth in a leaf infection assay. Upon induction with SA, TcNPR1 was shown to translocate into the nucleus of leaf and root cells in a manner identical to Arabidopsis NPR1. Cacao NPR1 was also capable of participating in SA-JA signaling crosstalk, as evidenced by the suppression of JA responsive gene expression in TcNPR1 overexpressing transgenic plants.

Conclusion
Our data indicate that the TcNPR1 is a functional ortholog of Arabidopsis NPR1, and is likely to play a major role in defense response in cacao. This fundamental knowledge can contribute to breeding of disease resistant cacao varieties through the application of molecular markers or the use of transgenic strategies.
An in silico analysis of the mitochondrial protein import apparatus of plants
Authors: Carrie Chris , Murcha Monika W , Whelan James 
Published: November 2010

Abstract

Background
An in silico analysis of the mitochondrial protein import apparatus from a variety of species; including Chlamydomonas reinhardtii, Chlorella variabilis, Ectocarpus siliculosus, Cyanidioschyzon merolae, Physcomitrella patens, Selaginella moellendorffii, Picea glauca, Oryza sativa and Arabidopsis thaliana was undertaken to determine if components differed within and between plant and non-plant species.

Results
The channel forming subunits of the outer membrane components Tom40 and Sam50 are conserved between plant groups and other eukaryotes. In contrast, the receptor component(s) in green plants, particularly Tom20, (C. reinhardtii, C. variabilis, P. patens, S. moellendorffii, P. glauca, O. sativa and A. thaliana) are specific to this lineage. Red algae contain a Tom22 receptor that is orthologous to yeast Tom22. Furthermore, plant mitochondrial receptors display differences between various plant lineages. These are evidenced by distinctive motifs in all plant Metaxins, which are absent in red algae, and the presence of the outer membrane receptor OM64 in Angiosperms (rice and Arabidopsis), but not in lycophytes (S. moellendorffii) and gymnosperms (P. glauca). Furthermore, although the intermembrane space receptor Mia40 is conserved across a wide phylogenetic range, its function differs between lineages. In all plant lineages, Tim17 contains a C-terminal extension, which may act as a receptor component for the import of nucleic acids into plant mitochondria.

Conclusions
It is proposed that the observed functional divergences are due to the selective pressure to sort proteins between mitochondria and chloroplasts, resulting in differences in protein receptor components between plant groups and other organisms. Additionally, diversity of receptor components is observed within the plant kingdom. Even when receptor components are orthologous across plant and non-plant species, it appears that the functions of these have expanded or diverged in a lineage specific manner.
Mining the bitter melon (momordica charantial.) seed transcriptome by 454 analysis of non-normalized and normalized cDNA populations for conjugated fatty acid metabolism-related genes
Authors: Yang Peizhen , Li Xiangjun , Shipp Matthew J , Shockey Jay M , Cahoon Edgar B 
Published: November 2010

Abstract

Background
Seeds of Momordica charantia (bitter melon) produce high levels of eleostearic acid, an unusual conjugated fatty acid with industrial value. Deep sequencing of non-normalized and normalized cDNAs from developing bitter melon seeds was conducted to uncover key genes required for biotechnological transfer of conjugated fatty acid production to existing oilseed crops. It is expected that these studies will also provide basic information regarding the metabolism of other high-value novel fatty acids.

Results
Deep sequencing using 454 technology with non-normalized and normalized cDNA libraries prepared from bitter melon seeds at 18 DAP resulted in the identification of transcripts for the vast majority of known genes involved in fatty acid and triacylglycerol biosynthesis. The non-normalized library provided a transcriptome profile of the early stage in seed development that highlighted the abundance of transcripts for genes encoding seed storage proteins as well as for a number of genes for lipid metabolism-associated polypeptides, including Δ12 oleic acid desaturases and fatty acid conjugases, class 3 lipases, acyl-carrier protein, and acyl-CoA binding protein. Normalization of cDNA by use of a duplex-specific nuclease method not only increased the overall discovery of genes from developing bitter melon seeds, but also resulted in the identification of 345 contigs with homology to 189 known lipid genes in Arabidopsis. These included candidate genes for eleostearic acid metabolism such as diacylglycerol acyltransferase 1 and 2, and a phospholipid:diacylglycerol acyltransferase 1-related enzyme. Transcripts were also identified for a novel FAD2 gene encoding a functional Δ12 oleic acid desaturase with potential implications for eleostearic acid biosynthesis.

Conclusions
454 deep sequencing, particularly with normalized cDNA populations, was an effective method for mining of genes associated with eleostearic acid metabolism in developing bitter melon seeds. The transcriptomic data presented provide a resource for the study of novel fatty acid metabolism and for the biotechnological production of conjugated fatty acids and possibly other novel fatty acids in established oilseed crops.
Significant association between polymorphism of the erythropoietin gene promoter and myelodysplastic syndrome
Authors: Ma Wanlong , Kantarjian Hagop , Zhang Ke , Zhang Xi , Wang Xiuqiang , Chen Clifford , Donahue Amber C , Zhang Zhong , Yeh Chen-Hsiung , O'Brien Susan , Garcia-Manero Guillermo , Caporaso Neil , Landgren Ola , Albitar Maher 
Published: November 2010

Abstract

Background
Myelodysplastic syndrome (MDS) may be induced by certain mutagenic environmental or chemotherapeutic toxins; however, the role of susceptibility genes remains unclear. The G/G genotype of the single-nucleotide polymorphism (SNP) rs1617640 in the erythropoietin (EPO) promoter has been shown to be associated with decreased EPO expression. We examined the association of rs1617640 genotype with MDS.

Methods
We genotyped the EPO rS1617640 SNP in 189 patients with MDS, 257 with acute myeloid leukemia (AML), 106 with acute lymphoblastic leukemia, 97 with chronic lymphocytic leukemia, 353 with chronic myeloid leukemia, and 95 healthy controls.

Results
The G/G genotype was significantly more common in MDS patients (47/187; 25.1%) than in controls (6/95; 6.3%) or in patients with other leukemias (101/813; 12.4%) (all P < 0.001). Individuals with the G/G genotype were more likely than those with other genotypes to have MDS (odd ratio = 4.98; 95% CI = 2.04-12.13). Clinical and follow up data were available for 112 MDS patients and 186 AML patients. There was no correlation between EPO promoter genotype and response to therapy or overall survival in MDS or AML. In the MDS group, the GG genotype was significantly associated with shorter complete remission duration, as compared with the TT genotype (P = 0.03). Time to neutrophils recovery after therapy was significantly longer in MDS patients with the G/G genotype (P = 0.02).

Conclusions
These findings suggest a strong association between the rs1617640 G/G genotype and MDS. Further studies are warranted to investigate the utility of screening for this marker in individuals exposed to environmental toxins or chemotherapy.
Tumour auto-antibody screening: performance of protein microarrays using SEREX derived antigens
Authors: Stempfer René , Syed Parvez , Vierlinger Klemens , Pichler Rudolf , Meese Eckart , Leidinger Petra , Ludwig Nicole , Kriegner Albert , Nöhammer Christa , Weinhäusel Andreas 
Published: November 2010

Abstract

Background
The simplicity and potential of minimal invasive testing using serum from patients make auto-antibody based biomarkers a very promising tool for use in diagnostics of cancer and auto-immune disease. Although several methods exist for elucidating candidate-protein markers, immobilizing these onto membranes and generating so called macroarrays is of limited use for marker validation. Especially when several hundred samples have to be analysed, microarrays could serve as a good alternative since processing macro membranes is cumbersome and reproducibility of results is moderate.

Methods
Candidate markers identified by SEREX (serological identification of antigens by recombinant expression cloning) screenings of brain and lung tumour were used for macroarray and microarray production. For microarray production recombinant proteins were expressed in E. coli by autoinduction and purified His-tag (histidine-tagged) proteins were then used for the production of protein microarrays. Protein arrays were hybridized with the serum samples from brain and lung tumour patients.

Result
Methods for the generation of microarrays were successfully established when using antigens derived from membrane-based selection. Signal patterns obtained by microarrays analysis of brain and lung tumour patients' sera were highly reproducible (R = 0.92-0.96). This provides the technical foundation for diagnostic applications on the basis of auto-antibody patterns. In this limited test set, the assay provided high reproducibility and a broad dynamic range to classify all brain and lung samples correctly.

Conclusion
Protein microarray is an efficient means for auto-antibody-based detection when using SEREX-derived clones expressing antigenic proteins. Protein microarrays are preferred to macroarrays due to the easier handling and the high reproducibility of auto-antibody testing. Especially when using only a few microliters of patient samples protein microarrays are ideally suited for validation of auto-antibody signatures for diagnostic purposes.
Utilization of delivery care among rural women in china: does the health insurance make a difference? a cross-sectional study
Authors: Xiao Shengbin , Yan Hong , Shen Yuan , Dang Shaonong , Hemminki Elina , Wang Duolao , Long Qian , Gao Jianmin 
Published: November 2010

Abstract

Background
Since 2003, the New Cooperative Medical Scheme (NCMS) has been implemented throughout rural China, usually covering delivery services in its benefit package. The objective of this study was to compare the difference of utilization of delivery services, expenditures, and local women's perceived affordability between women with and without reimbursement from NCMS.

Methods
A cross-sectional survey was carried out in two rural counties in Shaanxi province, China, during December 2008-March 2009. Women giving birth from April 2008 to March 2009 were interviewed by a structured questionnaire to collect information on utilization of delivery services. Multivariable analyses were used to compare the differences in outcomes between women with and without reimbursement from NCMS.

Results
Of the total 1613 women interviewed, 747(46.3%) got reimbursement to cover their expenditure on delivery care (NCMS group) and 866(53.7%) paid delivery services entirely out of their own pocket (Non-NCMS group). Compared with the Non-NCMS group, the NCMS group had significantly more women who delivered at hospital. The rate of Caesarean section (CS), proportion of women seeking higher level services, and length of hospitalization were similar between the two groups. The total hospital costs for delivery services in the NCMS group was significantly smaller and after being reimbursed, the out-of-pocket payment in the NCMS group was less than a half of that in the Non-NCMS group. Fewer women in the NCMS group than in the Non-NCMS group considered their payment for delivery services expensive.

Conclusions
There was no evidence of overuse delivery services among the women reimbursed by NCMS. Total hospital costs and women's costs for delivery services were found lower in the NCMS group, subsequently alleviation on women's perceived financial affordability.