bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractBackgroundWith 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.ResultsIn 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.ConclusionThe 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

Abstract

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

AbstractBackgroundTumor 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.MethodsMicroarrays 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.ResultsWhen 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.ConclusionThese 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

Abstract
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

AbstractBackgroundEpidemiologic 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.ResultsMice 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.ConclusionOur 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

Abstract
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

Abstract
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

Abstract
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

AbstractIn 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.
Heterogeneous expression of the adhesion receptor CD226 on murine NK and T cells and its function in NK-mediated killing of immature dendritic cells
Authors: Seth Sebastian , Georgoudaki Anna-Maria , Chambers Benedict J , Qiu Quan , Kremmer Elisabeth , Maier Michael K , Czeloth Niklas , Ravens Inga , Foerster Reinhold , Bernhardt Günter 
Published: April 2009

AbstractNewly generated monoclonal antibodies directed against murine CD226 define CD226/CD155-interaction in NK-mediated killing of immature dendritic cells.The adhesion receptor CD226 (DNAM-1) is a member of the Ig superfamily possessing two extracellular V-like domains. In humans, CD226 was shown to be expressed by NK as well as T cells. During T cell priming, CD226-mediated costimulatory signals may skew the subsequent differentiation into the Th1 pathway. In addition, CD226 expressed on NK and cytotoxic T cells is engaged by its counter-receptor CD155, present on target cells, thereby triggering their elimination. We established mAb specifically recognizing mCD226, demonstrating that CD226 is expressed by precursor and mature but not developing T cells. In contrast, NK cells are distinguished by a rather heterogeneous CD226 expression profile. In addition, expression of CD226 appears coupled to that of other NK cell receptors, as high expression of CD226 was found to correlate with decreased proportions of Ly49D and H positive NK cells. Upon injection into mice, the anti-CD226 antibodies caused selective depletion of CD8+ T cells. Moreover, these antibodies as well as a naturally occurring CD226 splice variant lacking the outermost V-like domain were instrumental in determining that CD226 adheres to CD155 via its first domain. In addition, antibodies were identified as capable of blocking the CD226/CD155 interaction and to prevent NK-driven killing of immature DC. CD226 is thus the first mNK receptor identified to be essential for the elimination of this particular cell type.
Prognostic Factors in Adult Patients up to 60 Years Old With Acute Myeloid Leukemia and Translocations of Chromosome Band 11q23: Individual Patient Data–Based Meta-Analysis of the German Acute Myeloid Leukemia Intergroup
Authors: Krauter Jürgen , Wagner Katharina , Schäfer Irina , Marschalek Rolf , Meyer Claus , Heil Gerhard , Schaich Markus , Ehninger Gerhard , Niederwieser Dietger , Krahl Rainer , Büchner Thomas , Sauerland Cristina , Schlegelberger Brigitte , Döhner Konstanze , Döhner Hartmut , Schlenk Richard F. , Ganser Arnold 
Published: April 2009

Purpose To identify risk factors for induction success and overall survival (OS) and relapse-free survival (RFS) and to evaluate the impact of allogeneic stem-cell transplantation (alloSCT) in adult patients up to 60 years old with acute myeloid leukemia (AML) and reciprocal translocations involving chromosome band 11q23 [t(11q23)]. Patients and Methods An individual patient data-based meta-analysis was performed on 180 adult patients with AML and t(11q23). These patients were identified by cytogenetics and/or molecular techniques and treated within eight prospective multicenter trials of the German AML Intergroup. The median follow-up time was 53 months. Results Complete remission rate was 71%. Favorable factors for induction success were the presence of a t(9;11), t(11q23) as a sole aberration, and de novo leukemia. OS rate at 4 years was 29%. Translocations other than t(9;11), platelets less than the median, secondary leukemia, and peripheral blasts greater than the median were adverse risk factors for OS. RFS rate at 4 years was 29%. The presence of a t(6;11) and peripheral blasts greater than the median had a negative impact on RFS. Three risk groups for OS and RFS could be defined by the combination of these factors with 4-year OS rates of 50%, 28%, and 5% and 4-year RFS rates of 37%, 26%, and 5%. An alloSCT from matched related or unrelated donors in first complete remission was beneficial, especially in t(6;11)-negative patients. Conclusion Risk stratification of AML patients with reciprocal translocations of chromosome band 11q23 is feasible based on the translocation partner and clinical parameters.