bluuebunny/crossref_metadata_2025 huggingface dataset:
Profile analysis and prediction of tissue-specific CpG island methylation classes
Authors: Previti Christopher , Harari Oscar , Zwir Igor , del Val Coral
Published: April 2009

Background

The computational prediction of DNA methylation has become an important topic in the recent years due to its role in the epigenetic control of normal and cancer-related processes. While previous prediction approaches focused merely on differences between methylated and unmethylated DNA sequences, recent experimental results have shown the presence of much more complex patterns of methylation across tissues and time in the human genome. These patterns are only partially described by a binary model of DNA methylation. In this work we propose a novel approach, based on profile analysis of tissue-specific methylation that uncovers significant differences in the sequences of CpG islands (CGIs) that predispose them to a tissue- specific methylation pattern.

Results

We defined CGI methylation profiles that separate not only between constitutively methylated and unmethylated CGIs, but also identify CGIs showing a differential degree of methylation across tissues and cell-types or a lack of methylation exclusively in sperm. These profiles are clearly distinguished by a number of CGI attributes including their evolutionary conservation, their significance, as well as the evolutionary evidence of prior methylation. Additionally, we assess profile functionality with respect to the different compartments of protein coding genes and their possible use in the prediction of DNA methylation.

Conclusion

Our approach provides new insights into the biological features that determine if a CGI has a functional role in the epigenetic control of gene expression and the features associated with CGI methylation susceptibility. Moreover, we show that the ability to predict CGI methylation is based primarily on the quality of the biological information used and the relationships uncovered between different sources of knowledge. The strategy presented here is able to predict, besides the constitutively methylated and unmethylated classes, two more tissue specific methylation classes conserving the accuracy provided by leading binary methylation classification methods.
ACID: annotation of cassette and integron data
Authors: Joss Michael J , Koenig Jeremy E , Labbate Maurizio , Polz Martin F , Gillings Michael R , Stokes Harold W , Doolittle W Ford , Boucher Yan
Published: April 2009

Background

Although integrons and their associated gene cassettes are present in ~10% of bacteria and can represent up to 3% of the genome in which they are found, very few have been properly identified and annotated in public databases. These genetic elements have been overlooked in comparison to other vectors that facilitate lateral gene transfer between microorganisms.

Description

By automating the identification of integron integrase genes and of the non-coding cassette-associated attC recombination sites, we were able to assemble a database containing all publicly available sequence information regarding these genetic elements. Specialists manually curated the database and this information was used to improve the automated detection and annotation of integrons and their encoded gene cassettes. ACID (annotation of cassette and integron data) can be searched using a range of queries and the data can be downloaded in a number of formats. Users can readily annotate their own data and integrate it into ACID using the tools provided.

Conclusion

ACID is a community resource providing easy access to annotations of integrons and making tools available to detect them in novel sequence data. ACID also hosts a forum to prompt integron-related discussion, which can hopefully lead to a more universal definition of this genetic element.
A bag-of-words approach for Drosophila gene expression pattern annotation
Authors: Ji Shuiwang , Li Ying-Xin , Zhou Zhi-Hua , Kumar Sudhir , Ye Jieping
Published: April 2009

Background

Drosophilagene expression pattern images document the spatiotemporal dynamics of gene expression during embryogenesis. A comparative analysis of these images could provide a fundamentally important way for studying the regulatory networks governing development. To facilitate pattern comparison and searching, groups of images in the BerkeleyDrosophilaGenome Project (BDGP) high-throughput study were annotated with a variable number of anatomical terms manually using a controlled vocabulary. Considering that the number of available images is rapidly increasing, it is imperative to design computational methods to automate this task.

Results

We present a computational method to annotate gene expression pattern images automatically. The proposed method uses the bag-of-words scheme to utilize the existing information on pattern annotation and annotates images using a model that exploits correlations among terms. The proposed method can annotate images individually or in groups (e.g., according to the developmental stage). In addition, the proposed method can integrate information from different two-dimensional views of embryos. Results on embryonic patterns from BDGP data demonstrate that our method significantly outperforms other methods.

Conclusion

The proposed bag-of-words scheme is effective in representing a set of annotations assigned to a group of images, and the model employed to annotate images successfully captures the correlations among different controlled vocabulary terms. The integration of existing annotation information from multiple embryonic views improves annotation performance.
Centrosome proteins form an insoluble perinuclear matrix during muscle cell differentiation
Authors: Srsen Vlastimil , Fant Xavier , Heald Rebecca , Rabouille Catherine , Merdes Andreas
Published: April 2009

Background

Muscle fibres are formed by elongation and fusion of myoblasts into myotubes. During this differentiation process, the cytoskeleton is reorganized, and proteins of the centrosome re-localize to the surface of the nucleus. The exact timing of this event, and the underlying molecular mechanisms are still poorly understood.

Results

We performed studies on mouse myoblast cell lines that were induced to differentiate in culture, to characterize the early events of centrosome protein re-localization. We demonstrate that this re-localization occurs already at the single cell stage, prior to fusion into myotubes. Centrosome proteins that accumulate at the nuclear surface form an insoluble matrix that can be reversibly disassembled if isolated nuclei are exposed to mitotic cytoplasm from Xenopus egg extract. Our microscopy data suggest that this perinuclear matrix of centrosome proteins consists of a system of interconnected fibrils.

Conclusion

Our data provide new insights into the reorganization of centrosome proteins during muscular differentiation, at the structural and biochemical level. Because we observe that centrosome protein re-localization occurs early during differentiation, we believe that it is of functional importance for the reorganization of the cytoskeleton in the differentiation process.
Mouse H6 Homeobox 1 (Hmx1) mutations cause cranial abnormalities and reduced body mass
Authors: Munroe Robert J , Prabhu Vinay , Acland Greg M , Johnson Kenneth R , Harris Belinda S , O'Brien Tim P , Welsh Ian C , Noden Drew M , Schimenti John C
Published: April 2009

Background

The H6 homeobox genes Hmx1, Hmx2, and Hmx3 (also known as Nkx5-3; Nkx5-2 and Nkx5-1, respectively), compose a family within the NKL subclass of the ANTP class of homeobox genes. Hmx gene family expression is mostly limited to sensory organs, branchial (pharyngeal) arches, and the rostral part of the central nervous system. Targeted mutation of either Hmx2 or Hmx3 in mice disrupts the vestibular system. These tandemly duplicated genes have functional overlap as indicated by the loss of the entire vestibular system in double mutants. Mutants have not been described for Hmx1, the most divergent of the family.

Results

Dumbo (dmbo) is a semi-lethal mouse mutation that was recovered in a forward genetic mutagenesis screen. Mutants exhibit enlarged ear pinnae with a distinctive ventrolateral shift. Here, we report on the basis of this phenotype and other abnormalities in the mutant, and identify the causative mutation as being an allele of Hmx1. Examination of dumbo skulls revealed only subtle changes in cranial bone morphology, namely hyperplasia of the gonial bone and irregularities along the caudal border of the squamous temporal bone. Other nearby otic structures were unaffected. The semilethality of dmbo/dmbo mice was found to be ~40%, occured perinatally, and was associated with exencephaly. Surviving mutants of both sexes exhibited reduced body mass from ~3 days postpartum onwards. Most dumbo adults were microphthalmic. Recombinant animals and specific deletion-bearing mice were used to map the dumbo mutation to a 1.8 Mb region on Chromosome 5. DNA sequencing of genes in this region revealed a nonsense mutation in the first exon of H6 Homeobox 1 (Hmx1; also Nkx5-3). An independent spontaneous allele called misplaced ears (mpe) was also identified, confirming Hmx1 as the responsible mutant gene.

Conclusion

The divergence of Hmx1 from its paralogs is reflected by different and diverse developmental roles exclusive of vestibular involvement. Additionally, these mutant Hmx1 alleles represent the first mouse models of a recently-discovered Oculo-Auricular syndrome caused by mutation of the orthologous human gene.
Natural variation of outcrossing in the hermaphroditic nematode Pristionchus pacificus
Authors: Click Arielle , Savaliya Chandni H , Kienle Simone , Herrmann Matthias , Pires-daSilva Andre
Published: April 2009

Background

Evolution of selfing can be associated with an increase in fixation of deleterious mutations, which in certain conditions can lead to species extinction. In nematodes, a few species evolved self-fertilization independently, making them excellent model systems to study the evolutionary consequences of this type of mating system.

Results

Here we determine various parameters that influence outcrossing in the hermaphroditic nematode Pristionchus pacificus and compare them to the better known Caenorhabditis elegans. These nematode species are distinct in terms of genetic diversity, which could be explained by differences in outcrossing rates. We find that, similarly to C. elegans, P. pacificus males are generated at low frequencies from self-fertilizing hermaphrodites and are relatively poor mating partners. Furthermore, crosses between different isolates reveal that hybrids have lower brood sizes than the pure strains, which is a sign of outbreeding depression. In contrast to C. elegans, P. pacificus has lower brood sizes and the male X-bearing sperm is able to outcompete the X-nullo sperm.

Conclusion

The results indicate that there is no evidence of any selection acting very strongly on P. pacificus males.
Functional annotation of the human retinal pigment epithelium transcriptome
Authors: Booij Judith C , van Soest Simone , Swagemakers Sigrid MA , Essing Anke HW , Verkerk Annemieke JMH , van der Spek Peter J , Gorgels Theo GMF , Bergen Arthur AB
Published: April 2009

Background

To determine level, variability and functional annotation of gene expression of the human retinal pigment epithelium (RPE), the key tissue involved in retinal diseases like age-related macular degeneration and retinitis pigmentosa. Macular RPE cells from six selected healthy human donor eyes (aged 63–78 years) were laser dissected and used for 22k microarray studies (Agilent technologies). Data were analyzed with Rosetta Resolver, the web tool DAVID and Ingenuity software.

Results

In total, we identified 19,746 array entries with significant expression in the RPE. Gene expression was analyzed according to expression levels, interindividual variability and functionality. A group of highly (n = 2,194) expressed RPE genes showed an overrepresentation of genes of the oxidative phosphorylation, ATP synthesis and ribosome pathways. In the group of moderately expressed genes (n = 8,776) genes of the phosphatidylinositol signaling system and aminosugars metabolism were overrepresented. As expected, the top 10 percent (n = 2,194) of genes with the highest interindividual differences in expression showed functional overrepresentation of the complement cascade, essential in inflammation in age-related macular degeneration, and other signaling pathways. Surprisingly, this same category also includes the genes involved in Bruch's membrane (BM) composition. Among the top 10 percent of genes with low interindividual differences, there was an overrepresentation of genes involved in local glycosaminoglycan turnover.

Conclusion

Our study expands current knowledge of the RPE transcriptome by assigning new genes, and adding data about expression level and interindividual variation. Functional annotation suggests that the RPE has high levels of protein synthesis, strong energy demands, and is exposed to high levels of oxidative stress and a variable degree of inflammation. Our data sheds new light on the molecular composition of BM, adjacent to the RPE, and is useful for candidate retinal disease gene identification or gene dose-dependent therapeutic studies.
Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli
Authors: Jin Ye , Watt Rory M , Danchin Antoine , Huang Jian-dong
Published: April 2009

Background

The low pH environment of the human stomach is lethal for most microorganisms; but notEscherichia coli, which can tolerate extreme acid stress. Acid resistance inE. coliis hierarchically controlled by numerous regulators among which are small noncoding RNAs (sncRNA).

Results

In this study, we individually deleted seventy-nine sncRNA genes from theE. coliK12-MG1655 chromosome, and established a single-sncRNA gene knockout library. By systematically screening the sncRNA mutant library, we show that the sncRNA GcvB is a novel regulator of acid resistance inE. coli. We demonstrate that GcvB enhances the ability ofE. colito survive low pH by upregulating the levels of the alternate sigma factor RpoS.

Conclusion

GcvB positively regulates acid resistance by affecting RpoS expression. These data advance our understanding of the sncRNA regulatory network involved in modulating acid resistance inE. coli.
The γ-gliadin multigene family in common wheat (Triticum aestivum) and its closely related species
Authors: Qi Peng-Fei , Wei Yu-Ming , Ouellet Thérèse , Chen Qing , Tan Xin , Zheng You-Liang
Published: April 2009

Background

The unique properties of wheat flour primarily depend on gluten, which is the most important source of protein for human being. γ-Gliadins have been considered to be the most ancient of the wheat gluten family. The complex family structure of γ-gliadins complicates the determination of their function. Moreover, γ-gliadins contain several sets of celiac disease epitopes. However, no systematic research has been conducted yet.

Results

A total of 170 γ-gliadin genes were isolated from common wheat and its closely related species, among which 138 sequences are putatively functional. The ORF lengths of these sequences range from 678 to 1089 bp, and the repetitive region is mainly responsible for the size heterogeneity of γ-gliadins. The repeat motif P(Q/L/S/T/I/V/R/A)F(S/Y/V/Q/I/C/L)P(R/L/S/T/H/C/Y)Q
1–2
(P(S/L/T/A/F/H)QQ)
1–2is repeated from 7 to 22 times. Sequence polymorphism and linkage disequilibrium analyses show that γ-gliadins are highly diverse. Phylogenic analyses indicate that there is no obvious discrimination between Sitopsis and Ae. tauschii at the Gli-1 loci, compared with diploid wheat. According to the number and placement of cysteine residues, we defined nine cysteine patterns and 17 subgroups. Alternatively, we classified γ-gliadins into two types based on the length of repetitive domain. Amino acid composition analyses indicate that there is a wide range of essential amino acids in γ-gliadins, and those γ-gliadins from subgroup SG-10 and SG-12 and γ-gliadins with a short repetitive domain are more nutritional. A screening of toxic epitopes shows that γ-gliadins with a pattern of C9 and γ-gliadins with a short repetitive domain almost lack any epitopes.

Conclusion

γ-Gliadin sequences in wheat and closely related Aegilops species are diverse. Each group/subgroup contributes differently to nutritional quality and epitope content. It is suggested that the genes with a short repetitive domain are more nutritional and valuable. Therefore, it is possible to breed wheat varieties, the γ-gliadins of which are less, even non-toxic and more nutritional.
Electro-acupuncture promotes survival, differentiation of the bone marrow mesenchymal stem cells as well as functional recovery in the spinal cord-transected rats
Authors: Ding Ying , Yan Qing , Ruan Jing-Wen , Zhang Yan-Qing , Li Wen-Jie , Zhang Yu-Jiao , Li Yan , Dong Hongxin , Zeng Yuan-Shan
Published: April 2009

Background

Bone marrow mesenchymal stem cells (MSCs) are one of the potential tools for treatment of the spinal cord injury; however, the survival and differentiation of MSCs in an injured spinal cord still need to be improved. In the present study, we investigated whether Governor Vessel electro-acupuncture (EA) could efficiently promote bone marrow mesenchymal stem cells (MSCs) survival and differentiation, axonal regeneration and finally, functional recovery in the transected spinal cord.

Results

The spinal cords of adult Sprague-Dawley (SD) rats were completely transected at T10, five experimental groups were performed: 1. sham operated control (Sham-control); 2. operated control (Op-control); 3. electro-acupuncture treatment (EA); 4. MSCs transplantation (MSCs); and 5. MSCs transplantation combined with electro-acupuncture (MSCs+EA). After 2-8 weeks of MSCs transplantation plus EA treatment, we found that the neurotrophin-3 (NT-3), cAMP level, the differentiation of MSCs, the 5-HT positive and CGRP positive nerve fibers in the lesion site and nearby tissue of injured spinal cord were significantly increased in the MSCs+EA group as compared to the group of the MSCs transplantation or the EA treated alone. Furthermore, behavioral test and spinal cord evoked potentials detection demonstrated a significantly functional recovery in the MSCs +EA group.

Conclusion

These results suggest that EA treatment may promote grafted MSCs survival and differentiation; MSCs transplantation combined with EA treatment could promote axonal regeneration and partial locomotor functional recovery in the transected spinal cord in rats and indicate a promising avenue of treatment of spinal cord injury.
Reasons of general practitioners for not prescribing lipid-lowering medication to patients with diabetes: a qualitative study
Authors: AB Elisabeth , Denig Petra , van Vliet Ton , Dekker Janny H
Published: April 2009

Background

Lipid-lowering medication remains underused, even in high-risk populations. The objective of this study was to determine factors underlying general practitioners' decisions not to prescribe such drugs to patients with type 2 diabetes.

Methods

A qualitative study with semi-structured interviews using real cases was conducted to explore reasons for not prescribing lipid-lowering medication after a guideline was distributed that recommended the use of statins in most patients with type 2 diabetes. Seven interviews were conducted with general practitioners (GPs) in The Netherlands, and analysed using an analytic inductive approach.

Results

Reasons for not-prescribing could be divided into patient and physician-attributed factors. According to the GPs, some patients do not follow-up on agreed medication and others object to taking lipid-lowering medication, partly for legitimate reasons such as expected or perceived side effects. Furthermore, the GPs themselves perceived reservations for prescribing lipid-lowering medication in patients with short life expectancy, expected compliance problems or near goal lipid levels. GPs sometimes postponed the start of treatment because of other priorities. Finally, barriers were seen in the GPs' practice organisation, and at the primary-secondary care interface.

Conclusion

Some of the barriers mentioned by GPs seem to be valid reasons, showing that guideline non-adherence can be quite rational. On the other hand, treatment quality could improve by addressing issues, such as lack of knowledge or motivation of both the patient and the GP. More structured management in general practice may also lead to better treatment.
Activation of P2X7-mediated apoptosis Inhibits DMBA/TPA-induced formation of skin papillomas and cancer in mice
Authors: Fu Wen , McCormick Tom , Qi Xiaoping , Luo Liping , Zhou Lingyin , Li Xin , Wang Bing-Cheng , Gibbons Heidi E , Abdul-Karim Fadi W , Gorodeski George I
Published: April 2009

Background

The study tested the hypothesis that apoptosis can prevent and control growth of neoplastic cells. Previous studies in-vitro have shown that the pro-apoptotic P2X7receptor regulates growth of epithelial cells. The specific objective of the present study was to understand to what degree the P2X7system controls development and growth of skin cancer in vivo, and what cellular and molecular mechanisms are involved in the P2X7action.

Methods

Skin neoplasias in mice (papillomas, followed by squamous spindle-cell carcinomas) were induced by local application of DMBA/TPA. Experiments in-vitro utilized cultured epidermal keratinocytes generated from wild-type or from P2X7-null mice. Assays involved protein immunostaining and Western blots; mRNA real-time qPCR; and apoptosis (evaluated in situ by TUNEL and quantified in cultured keratinocytes as solubilized DNA or by ELISA). Changes in cytosolic calcium or in ethidium bromide influx (P2X7pore formation) were determined by confocal laser microscopy.

Results

(a) Co-application on the skin of the P2X7specific agonist BzATP inhibited formation of DMBA/TPA-induced skin papillomas and carcinomas. At the completion of study (week 28) the proportion of living animals with cancers in the DMBA/TPA group was 100% compared to 43% in the DMBA/TPA+BzATP group. (b) In the normal skin BzATP affected mainly P2X7-receptor – expressing proliferating keratinocytes, where it augmented apoptosis without evoking inflammatory changes. (c) In BzATP-treated mice the degree of apoptosis was lesser in cancer than in normal or papilloma keratinocytes. (d) Levels of P2X7receptor, protein and mRNA were 4–5 fold lower in cancer tissues than in normal mouse tissues. (e) In cultured mouse keratinocytes BzATP induced apoptosis, formation of pores in the plasma membrane, and facilitated prolonged calcium influx. (f) The BzATP-induced apoptosis, pore-formation and augmented calcium influx had similar dose-dependence for BzATP. (g) Pore formation and the augmented calcium influx were depended on the expression of the P2X7receptor, while the BzATP-induced apoptosis depended on calcium influx. (h) The BzATP-induced apoptosis could be blocked by co-treatment with inhibitors of caspase-9 and caspase-3, but not of caspase-8.

Conclusion

(a) P2X7-dependent apoptosis is an important mechanism that controls the development and progression of epidermal neoplasia in the mouse. (b) The P2X7-dependent apoptosis is mediated by calcium influx via P2X7pores, and involves the caspase-9 (mitochondrial) pathway. (c) The diminished pro-apoptotic effect of BzATP in mouse cancer keratinocytes is possibly the result of low expression of the P2X7receptor. (d) Activation of P2X7-dependent apoptosis, e.g. with BzATP could be a novel chemotherapeutic growth-preventive modality for papillomas and epithelial cancers in vivo.
A comparison of synthetic oligodeoxynucleotides, DNA fragments and AAV-1 for targeted episomal and chromosomal gene repair
Authors: Leclerc Xavier , Danos Olivier , Scherman Daniel , Kichler Antoine
Published: April 2009

Background

Current strategies for gene therapy of inherited diseases consist in adding functional copies of the gene that is defective. An attractive alternative to these approaches would be to correct the endogenous mutated gene in the affected individual. This study presents a quantitative comparison of the repair efficiency using different forms of donor nucleic acids, including synthetic DNA oligonucleotides, double stranded DNA fragments with sizes ranging from 200 to 2200 bp and sequences carried by a recombinant adeno-associated virus (rAAV-1). Evaluation of each gene repair strategy was carried out using two different reporter systems, a mutated eGFP gene or a dual construct with a functional eGFP and an inactive luciferase gene, in several different cell systems. Gene targeting events were scored either following transient co-transfection of reporter plasmids and donor DNAs, or in a system where a reporter construct was stably integrated into the chromosome.

Results

In both episomal and chromosomal assays, DNA fragments were more efficient at gene repair than oligonucleotides or rAAV-1. Furthermore, the gene targeting frequency could be significantly increased by using DNA repair stimulating drugs such as doxorubicin and phleomycin.

Conclusion

Our results show that it is possible to obtain repair frequencies of 1% of the transfected cell population under optimized transfection protocols when cells were pretreated with phleomycin using rAAV-1 and dsDNA fragments.
Gene Composer: database software for protein construct design, codon engineering, and gene synthesis
Authors: Lorimer Don , Raymond Amy , Walchli John , Mixon Mark , Barrow Adrienne , Wallace Ellen , Grice Rena , Burgin Alex , Stewart Lance
Published: April 2009

Background

To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering.

Results

An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies.

Conclusion

We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease error correction in combination with PIPE cloning. In a sister manuscript we present data on how Gene Composer designed genes and protein constructs can result in improved protein production for structural studies.
Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer
Authors: Raymond Amy , Lovell Scott , Lorimer Don , Walchli John , Mixon Mark , Wallace Ellen , Thompkins Kaitlin , Archer Kimberly , Burgin Alex , Stewart Lance
Published: April 2009

Background

With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript.

Results

In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38α), viral polymerase (HCV NS5B), and bacterial structural protein (FtsZ) were expressed in bothE. coliand a cell-free wheat germ translation system. We also compare the protein expression levels inE. colifor a set of 11 different proteins with greatly varied G:C content and codon bias.

Conclusion

The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ fromBacillus subtilis. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.
Morphological features and differential counts of Plasmodium knowles i parasites in naturally acquired human infections
Authors: Lee Kim-Sung , Cox-Singh Janet , Singh Balbir
Published: April 2009

Background

Human infections with Plasmodium knowlesi, a simian malaria parasite, are more common than previously thought. They have been detected by molecular detection methods in various countries in Southeast Asia, where they were initially diagnosed by microscopy mainly as Plasmodium malariae and at times, as Plasmodium falciparum. There is a paucity of information on the morphology of P. knowlesi parasites and proportion of each erythrocytic stage in naturally acquired human infections. Therefore, detailed descriptions of the morphological characteristics and differential counts of the erythrocytic stages of P. knowlesi parasites in human infections were made, photographs were taken, and morphological features were compared with those of P. malariae and P. falciparum.

Methods

Thick and thin blood films were made prior to administration of anti-malarial treatment in patients who were subsequently confirmed as having single species knowlesi infections by PCR assays. Giemsa-stained blood films, prepared from 10 randomly selected patients with a parasitaemia ranging from 610 to 236,000 parasites per μl blood, were examined.

Results

The P. knowlesi infection was highly synchronous in only one patient, where 97% of the parasites were at the late trophozoite stage. Early, late and mature trophozoites and schizonts were observed in films from all patients except three; where schizonts and early trophozoites were absent in two and one patient, respectively. Gametocytes were observed in four patients, comprising only between 1.2 to 2.8% of infected erythrocytes. The early trophozoites of P. knowlesi morphologically resemble those of P. falciparum. The late and mature trophozoites, schizonts and gametocytes appear very similar to those of P. malariae. Careful examinations revealed that some minor morphological differences existed between P. knowlesi and P. malariae. These include trophozoites of knowlesi with double chromatin dots and at times with two or three parasites per erythrocyte and mature schizonts of P. knowlesi having 16 merozoites, compared with 12 for P. malariae.

Conclusion

Plasmodium knowlesi infections in humans are not highly synchronous. The morphological resemblance of early trophozoites of P. knowlesi to P. falciparum and later erythrocytic stages to P. malariae makes it extremely difficult to identify P. knowlesi infections by microscopy alone.
A compact VEGF signature associated with distant metastases and poor outcomes
Authors: Hu Zhiyuan , Fan Cheng , Livasy Chad , He Xiaping , Oh Daniel S , Ewend Matthew G , Carey Lisa A , Subramanian Subbaya , West Robert , Ikpatt Francis , Olopade Olufunmilayo I , van de Rijn Matt , Perou Charles M
Published: April 2009

Background

Tumor metastases pose the greatest threat to a patient's survival, and thus, understanding the biology of disseminated cancer cells is critical for developing effective therapies.

Methods

Microarrays and immunohistochemistry were used to analyze primary breast tumors, regional (lymph node) metastases, and distant metastases in order to identify biological features associated with distant metastases.

Results

When compared with each other, primary tumors and regional metastases showed statistically indistinguishable gene expression patterns. Supervised analyses comparing patients with distant metastases versus primary tumors or regional metastases showed that the distant metastases were distinct and distinguished by the lack of expression of fibroblast/mesenchymal genes, and by the high expression of a 13-gene profile (that is, the 'vascular endothelial growth factor (VEGF) profile') that includedVEGF, ANGPTL4, ADMand the monocarboxylic acid transporterSLC16A3. At least 8 out of 13 of these genes contained HIF1α binding sites, many are known to be HIF1α-regulated, and expression of the VEGF profile correlated with HIF1α IHC positivity. The VEGF profile also showed prognostic significance on tests of sets of patients with breast and lung cancer and glioblastomas, and was an independent predictor of outcomes in primary breast cancers when tested in models that contained other prognostic gene expression profiles and clinical variables.

Conclusion

These data identify a compactin vivohypoxia signature that tends to be present in distant metastasis samples, and which portends a poor outcome in multiple tumor types.

This signature suggests that the response to hypoxia includes the ability to promote new blood and lymphatic vessel formation, and that the dual targeting of multiple cell types and pathways will be needed to prevent metastatic spread.
The genome and proteome of a virulent Escherichia coli O157:H7 bacteriophage closely resembling Salmonella phage Felix O1
Authors: Villegas Andre , She Yi-Min , Kropinski Andrew M , Lingohr Erika J , Mazzocco Amanda , Ojha Shivani , Waddell Thomas E , Ackermann Hans-Wolfgang , Moyles Dianne M , Ahmed Rafiq , Johnson Roger P
Published: April 2009

Based upon whole genome and proteome analysis, Escherichia coli O157:H7-specific bacteriophage (phage) wV8 belongs to the new myoviral genus, "the Felix O1-like viruses" along with Salmonella phage Felix O1 and Erwinia amylovora phage φEa21-4. The genome characteristics of phage wV8 (size 88.49 kb, mol%G+C 38.9, 138 ORFs, 23 tRNAs) are very similar to those of phage Felix O1 (86.16 kb, 39.0 mol%G+C, 131 ORFs and 22 tRNAs) and, indeed most of the proteins have their closest homologs within Felix O1. Approximately one-half of the Escherichia coli O157:H7 mutants resistant to phage wV8 still serotype as O157:H7 indicating that this phage may recognize, like coliphage T4, two different surface receptors: lipopolysaccharide and, perhaps, an outer membrane protein.
Lack of acute phase response in the livers of mice exposed to diesel exhaust particles or carbon black by inhalation
Authors: Saber Anne T , Halappanavar Sabina , Folkmann Janne K , Bornholdt Jette , Boisen Anne Mette Z Z , Møller Peter , Williams Andrew , Yauk Carole , Vogel Ulla , Loft Steffen , Wallin Håkan
Published: April 2009

Background

Epidemiologic and animal studies have shown that particulate air pollution is associated with increased risk of lung and cardiovascular diseases. Although the exact mechanisms by which particles induce cardiovascular diseases are not known, studies suggest involvement of systemic acute phase responses, including C-reactive protein (CRP) and serum amyloid A (SAA) in humans. In this study we test the hypothesis that diesel exhaust particles (DEP) – or carbon black (CB)-induced lung inflammation initiates an acute phase response in the liver.

Results

Mice were exposed to filtered air, 20 mg/m3DEP or CB by inhalation for 90 minutes/day for four consecutive days; we have previously shown that these mice exhibit pulmonary inflammation (Saber AT, Bornholdt J, Dybdahl M, Sharma AK, Loft S, Vogel U, Wallin H. Tumor necrosis factor is not required for particle-induced genotoxicity and pulmonary inflammation., Arch. Toxicol. 79 (2005) 177–182). As a positive control for the induction of an acute phase response, mice were exposed to 12.5 mg/kg of lipopolysaccharide (LPS) intraperitoneally. Quantitative real time RT-PCR was used to examine the hepatic mRNA expression of acute phase proteins, serum amyloid P (Sap) (the murine homologue ofCrp) andSaa1andSaa3. While significant increases in the hepatic expression ofSap, Saa1andSaa3were observed in response to LPS, their levels did not change in response to DEP or CB. In a comprehensive search for markers of an acute phase response, we analyzed liver tissue from these mice using high density DNA microarrays. Globally, 28 genes were found to be significantly differentially expressed in response to DEP or CB. The mRNA expression of three of the genes (serine (or cysteine) proteinase inhibitor, clade A, member 3C, apolipoprotein E and transmembrane emp24 domain containing 3) responded to both exposures. However, these changes were very subtle and were not confirmed by real time RT-PCR.

Conclusion

Our findings collectively suggest thatSap, Saa1andSaa3are not induced in livers of mice exposed to DEP or CB. Despite pulmonary inflammation in these mice, global transcriptional profiling of liver did not reveal any hepatic response following exposure by inhalation.
Behavioural and Electrophysiological Characterisation of Experimentally Induced Osteoarthritis and Neuropathy in C57Bl/6 Mice
Authors: Harvey Victoria L , Dickenson Anthony H
Published: April 2009

Background

Osteoarthritis is a widespread condition affecting the elderly where ~70–90% of over 75 year olds are affected, representing one of the largest cost burdens to healthcare in the western world. The monosodium iodoacetate (MIA) osteoarthritis model has been well described in the rat especially in terms of the pathological progression of the disease and more recently pain behaviour. In this study, we characterise, for the first time, MIA induced osteoarthritis in mice and compare it with nerve-injured mice (partial sciatic nerve injury), using both behavioural and in vivo electrophysiological measurements. These approaches uniquely allow the threshold and suprathreshold measures to many modalities to be quantified and so form a basis for improving and expanding transgenic studies.

Results

Significant mechanical hypersensitivity was observed in the ipsilateral hindpaw in MIA injected mice at all observed time points following infrapetellar MIA injection (p < 0.05). The mechanical hypersensitivity exhibited a partial biphasic temporal pattern, but thermal hypersensitivity was absent. Electrically-evoked dorsal horn neuronal responses in MIA injected mice were significantly elevated (p < 0.05) with respect to A- and C-fibre firing, input, pinch and noxious von Frey (26 and 60 g). No significant changes in A- or C-fibre thresholds were observed. Nerve-injured mice displayed significant behavioural thermal and mechanical hypersensitivity (p < 0.05) and evoked dorsal horn responses were significantly increased with respect to C-fibre firing, pinch and wind-up (p < 0.05).

Conclusion

The MIA model of osteoarthritic pain in mice displays behavioural characteristics similar to those observed in rats. Changes in both behavioural measures and neuronal activity from the paw, suggest that central changes are involved in this pain state, although a role for peripheral drives is also likely. Moreover, the behavioural and neuronal measures in these two pain models showed overlapping alterations in terms of certain neuronal measures and mechanical sensitivity despite their very different pathologies and a loss of input in neuropathy, suggesting some commonalities in the central processing of different peripheral pain states. This murine model of osteoarthritis will allow the exploitation of knock out animals to better understand underlying mechanisms and identify novel molecular targets.
Age distribution and gender differences in psychogenic fever patients
Authors: Kaneda Yuko , Tsuji Sadatoshi , Oka Takakazu
Published: April 2009

Psychogenic fever is one of the most common psychosomatic diseases. In Japan, psychogenic fever has generally been reported to occur in adolescents, with a peak seen at age 13. However, in our department we have encountered many adults with psychogenic fever. Therefore, we investigated all outpatients who visited the Psychosomatic Department of the University of Occupational and Environmental Health between April 2003 and March 2007. Of the 2705 outpatients that were seen, 55 patients (2.0%) were diagnosed with psychogenic fever. The patients ranged in age from 11 to 82 years old, with a mean age of 33.6 ± 17.9 (mean ± SD) years. In addition to the adolescents, many of the patients were in their 20 s and 30 s, and the male:female ratio was 1:2.2. This study suggests that psychogenic fever commonly occurs not only in adolescents but also in adults.
Serum proteomic profiling and haptoglobin polymorphisms in patients with GVHD after allogeneic hematopoietic cell transplantation
Authors: McGuirk Joseph , Hao Gang , Hou Weijian , Abhyankar Sunil , Williams Casey , Yan Weisi , Yuan Jianda , Guan Xiuqin , Belt Robert , Dejarnette Shaun , Wieman Jeffery , Yan Ying
Published: April 2009

We studied serum proteomic profiling in patients with graft versus host disease (GVHD) after allogeneic hematopoietic cell transplantation (allo-HCT) by two-dimensional gel electrophoresis (2-DE) and mass spectrometry analysis. The expression of a group of proteins, haptoglobin (Hp), alpha-1-antitrypsin, apolipoprotein A-IV, serum paraoxonase and Zn-alpha-glycoprotein were increased and the proteins, clusterin precursor, alpha-2-macroglobulin, serum amyloid protein precursor, sex hormone-binding globulin, serotransferrin and complement C4 were decreased in patients with extensive chronic GVHD (cGVHD). Serum haptoglobin (Hp) levels in patients with cGVHD were demonstrated to be statistically higher than in patients without cGVHD and normal controls (p < 0.01). We used immunoblotting and PCR in combination with 2-DE gel image analysis to determine Hp polymorphisms in 25 allo-HCT patients and 16 normal donors. The results demonstrate that patients with cGVHD had a higher incidence of HP 2-2 phenotype (43.8%), in comparison to the patients without cGVHD (0%) and normal donors (18.7%), suggesting the possibility that specific Hp polymorphism may play a role in the development of cGVHD after allo-HCT. In this study, quantitative serum Hp levels were shown to be related to cGVHD development. Further, the data suggest the possibility that specific Hp polymorphisms may be associated with cGVHD development and warrant further investigation.
Differential gene expression in the salivary gland during development and onset of xerostomia in Sjögren's syndrome-like disease of the C57BL/6.NOD-Aec1Aec2mouse
Authors: Nguyen Cuong Q , Sharma Ashok , Lee Byung Ha , She Jin-Xiong , McIndoe Richard A , Peck Ammon B
Published: April 2009

Introduction

Recently, we reported the development of the C57BL/6.NOD-Aec1Aec2 mouse that carries two genetic intervals derived from the non-obese diabetic (NOD) mouse capable of conferring Sjögren's syndrome (SjS)-like disease in SjS-non-susceptible C57BL/6 mice. In an attempt to define the molecular bases underlying the onset of stomatitis sicca (xerostomia) in this C57BL/6.NOD-Aec1Aec2 mouse model, we have carried out a study using genomic microarray technology.

Methods

By means of oligonucleotide microarrays, gene expression profiles of salivary glands at 4, 8, 12, 16, and 20 weeks of age were generated for C57BL/6.NOD-Aec1Aec2 male mice. Using Linear Models for Microarray Analysis and B-statistics software, 480 genes were identified as being differentially expressed (P < 0.01 and Q < 0.0001) during the development of SjS-like disease in the salivary glands.

Results

The 480 genes could be arranged into four clusters, with each cluster defining a unique pattern of temporal expression, while the individual genes within each cluster could be grouped according to related biological functions. By means of pair-wise analysis, temporal changes in transcript expressions provided profiles indicating that many additional genes are differentially expressed at specific time points during the development of disease. Multiple genes reportedly showing an association with autoimmunity and/or SjS, in either humans or mouse models, were found to exhibit differential expressions, both quantitatively and temporally. Selecting various families of genes associated with specific functions (for example, antibody production, complement, and chemokines), we noted that only a limited number of family members showed differential expressions and these correlated with specific phases of disease.

Conclusions

Taking advantage of known functions of these genes, investigators can construct interactive gene pathways, leading to modeling of possible underlying events inducing salivary gland dysfunction. Thus, these different approaches to analyzing microarray data permit the identification of multiple sets of genes of interest whose expressions and expression profiles may correlate with molecular mechanisms, signaling pathways, and/or immunological processes involved in the development and onset of SjS.
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
Authors: Kawaji Hideya , Severin Jessica , Lizio Marina , Waterhouse Andrew , Katayama Shintaro , Irvine Katharine M , Hume David A , Forrest Alistair RR , Suzuki Harukazu , Carninci Piero , Hayashizaki Yoshihide , Daub Carsten O
Published: April 2009

In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along a differentiation time course of the human THP-1 cell line and under 52 systematic siRNA perturbations. In addition, data regarding chromatin status derived from ChIP-chip to elucidate the transcriptional regulatory interactions are included. Here we present these data to the research community as an integrated web resource.