bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and Initial Validation of a Measure of Academic Behaviors Associated With College and Career Readiness
Authors: Lombardi Allison , Seburn Mary , Conley David
Published: May 2011

In this cross-validation study, the authors examined the psychometric properties of a measure of academic behaviors associated with college and career readiness intended for high school students. An exploratory factor analysis (EFA) was conducted with a randomly selected portion of the sample ( n = 413) and resulted in four reliable factors: Goal-driven Behaviors, Persistence, Study Skills, and Self-Monitoring. A confirmatory factor analysis was conducted with the remaining sample ( n = 610). Goodness-of-fit indices indicated acceptable model fit. Follow-up analyses revealed significant differences in factor scores among 9th grade students according to gender and race but no significant differences between students in grades 10 through 12, showing the measure functions similarly across students for the most part and particularly for students approaching graduation. Implications for use as a value-added assessment in secondary environments are discussed.
Porosity and cutting forces: from macroscale to microscale machining correlations
Authors: Tutunea-Fatan O R , Fakhri M A , Bordatchev E V
Published: May 2011

Porous metals, typically produced through powder metallurgy, represent a class of relatively new materials with wide industrial applications, lately extending into the microscale domain. Although produced in near-net shapes, most components fabricated from these materials still require some form of secondary machining. Despite the progress made in the field, relatively little is known either on the inherent cutting mechanism or on the behaviour of these materials under micromachining conditions. The present study reviews the main cutting theories proposed in macroscale machining, along with one of the primary parameters used to describe its machinability performances, namely cutting forces. Then, the feasibility of macroscale concepts is discussed in the context of micromachining technology that is characterized by comparable tool and pore sizes. The microslot cutting experiment performed in a porous titanium sample outlined the relative interplay between the magnitude of the cutting force and porosity of the material. Based on this, it was concluded that the impact of structural porosity on cutting forces experienced during micromachining is significant and therefore further in-depth investigations will be required.
Application of continuous spindle speed variation for chatter avoidance in roughing milling
Authors: Bediaga I , Zatarain M , Muñoa J , Lizarralde R
Published: May 2011

This paper investigates the effectiveness of the continuous spindle speed variation (CSSV) technique as a chatter-suppression strategy in the milling process. For this purpose, a two-fold study was carried out: on the one hand, a simulation analysis, and on the other, experimental tests. First, the semidiscretization method has been extended to n-mode systems in any spatial direction and modified to include simulation capabilities concerning spindle speed variation with different waveforms. A new kind of stability map for different amplitude and frequency variations is proposed in order to optimize the parameter selection when machining. Finally, the effectiveness of the CSSV technique is verified through experimental tests.
Curve fabrication model analysis of near-field photolithography
Authors: Lin Z-C , Yang C-B
Published: May 2011

The Levenberg–Marquardt method is used to interpolate within the allowable maximum confined chord error through reasonable convergence criteria, to ensure that the geometric error of the designed and fabricated curves of near-field photolithography, constructed and planned with micro-lines segments, lie within an acceptable range. Meanwhile, the exposure energy density of the interpolated point during the fibre probe scan turning is integrated and added when processing two micro-lines, to create a method for analysing the exposure energy density of curve fabrication. Finally, the simulation in this paper shows that, during photolithographic curve fabrication, the contours of exposure energy density of the convex curvature of similar curves made by various micro-lines tend to face the fabrication central line. Therefore, the fabrication line tends to move towards concave curvature, and diffuses towards concave curvature. The depth of the simulated fabrication curve increases, whereas the full-width at half maximum (FWHM) decreases.
Pharmacogenomics of bortezomib test-dosing identifies hyperexpression of proteasome genes, especially PSMD4, as novel high-risk feature in myeloma treated with Total Therapy 3
Authors: Shaughnessy John D. , Qu Pingping , Usmani Saad , Heuck Christoph J. , Zhang Qing , Zhou Yiming , Tian Erming , Hanamura Ichiro , van Rhee Frits , Anaissie Elias , Epstein Joshua , Nair Bijay , Stephens Owen , Williams Ryan , Waheed Sarah , Alsayed Yazan , Crowley John , Barlogie Bart
Published: May 2011

Gene expression profiling (GEP) of purified plasma cells 48 hours after thalidomide and dexamethasone test doses showed these agents' mechanisms of action and provided prognostic information for untreated myeloma patients on Total Therapy 2 (TT2). Bortezomib was added in Total Therapy 3 (TT3), and 48 hours after bortezomib GEP analysis identified 80 highly survival-discriminatory genes in a training set of 142 TT3A patients that were validated in 128 patients receiving TT3B. The 80-gene GEP model (GEP80) also distinguished outcomes when applied at baseline in both TT3 and TT2 protocols. In context of our validated 70-gene model (GEP70), the GEP80 model identified 9% of patients with a grave prognosis among those with GEP70-defined low-risk disease and 41% of patients with favorable prognosis among those with GEP70-defined high-risk disease. PMSD4 was 1 of 3 genes common to both models. Residing on chromosome 1q21, PSMD4 expression is highly sensitive to copy number. Both higher PSMD4 expression levels and higher 1q21 copy numbers affected clinical outcome adversely. GEP80 baseline-defined high risk, high lactate dehydrogenase, and low albumin were the only independent adverse variables surviving multivariate survival model. We are investigating whether second-generation proteasome inhibitors (eg, carfilzomib) can overcome resistance associated with high PSMD4 levels.
MiR-17/20/93/106 promote hematopoietic cell expansion by targeting sequestosome 1–regulated pathways in mice
Authors: Meenhuis Annemarie , van Veelen Peter A. , de Looper Hans , van Boxtel Nicole , van den Berge Iris J. , Sun Su M. , Taskesen Erdogan , Stern Patrick , de Ru Arnoud H. , van Adrichem Arjan J. , Demmers Jeroen , Jongen-Lavrencic Mojca , Löwenberg Bob , Touw Ivo P. , Sharp Phillip A. , Erkeland Stefan J.
Published: May 2011

MicroRNAs (miRNAs) are pivotal for regulation of hematopoiesis but their critical targets remain largely unknown. Here, we show that ectopic expression of miR-17, -20,-93 and -106, all AAAGUGC seed-containing miRNAs, increases proliferation, colony outgrowth and replating capacity of myeloid progenitors and results in enhanced P-ERK levels. We found that these miRNAs are endogenously and abundantly expressed in myeloid progenitors and down-regulated in mature neutrophils. Quantitative proteomics identified sequestosome 1 (SQSTM1), an ubiquitin-binding protein and regulator of autophagy-mediated protein degradation, as a major target for these miRNAs in myeloid progenitors. In addition, we found increased expression of Sqstm1 transcripts during CSF3-induced neutrophil differentiation of 32D-CSF3R cells and an inverse correlation of SQSTM1 protein levels and miR-106 expression in AML samples. ShRNA-mediated silencing of Sqstm1 phenocopied the effects of ectopic miR-17/20/93/106 expression in hematopoietic progenitors in vitro and in mice. Further, SQSTM1 binds to the ligand-activated colony-stimulating factor 3 receptor (CSF3R) mainly in the late endosomal compartment, but not in LC3 positive autophagosomes. SQSTM1 regulates CSF3R stability and ligand-induced mitogen-activated protein kinase signaling. We demonstrate that AAAGUGC seed-containing miRNAs promote cell expansion, replating capacity and signaling in hematopoietic cells by interference with SQSTM1-regulated pathways.
Engineering Klebsiella sp. 601 multicopper oxidase enhances the catalytic efficiency towards phenolic substrates
Authors: Li Yadong , Gong Zijun , Li Xin , Li Yang , Wang Xing-Guo
Published: May 2011

Background

Structural comparison between bacterial CueO and fungal laccases has suggested that a charged residue Glu (E106) in CueO replaces the corresponding residue Phe in fungal laccases at the gate of the tunnel connecting type II copper to the protein surface and an extra α-helix (L351-G378) near the type I copper site covers the substrate binding pocket and might compromise the electron transfer from substrate to type I copper. To test this hypothesis, several mutants were made in Klebsiella sp. 601 multicopper oxidase, which is highly homologous to E. coli CueO with a similarity of 90% and an identity of 78%.

Results

The E106F mutant gave smaller K

m
(2.4-7fold) and k

cat
(1-4.4 fold) values for all three substrates DMP, ABTS and SGZ as compared with those for the wild-type enzyme. Its slightly larger k

cat

/K

m
values for three substrates mainly come from the decreased K

m
. Deleting α-helix (L351-G378) resulted in the formation of inactive inclusion body when the mutant Δα351-378 was expressed in E. coli. Another mutant α351-380M was then made via substitution of seven amino acid residues in the α-helix (L351-G378) region. The α351-380M mutant was active, and displayed a far-UV CD spectrum markedly different from that for wild-type enzyme. Kinetic studies showed the α351-380M mutant gave very low K

m
values for DMP, ABTS and SGZ, 4.5-, 1.9- and 7-fold less than those for the wild type. In addition, k

cat

/K

m
values were increased, 9.4-fold for DMP, similar for ABTS and 3-fold for SGZ.

Conclusion

The Glu residue at position 106 appears not to be the only factor affecting the copper binding, and it may also play a role in maintaining enzyme conformation. The α-helix (L351-G378) may not only block access to the type I copper site but also play a role in substrate specificities of bacterial MCOs. The α351-380M mutant catalyzing oxidation of the phenolic substrate DMP effectively would be very useful in green chemistry.
RAG: An update to the RNA-As-Graphs resource
Authors: Izzo Joseph A , Kim Namhee , Elmetwaly Shereef , Schlick Tamar
Published: May 2011

Background

In 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structure motifs using clustering and build-up approaches. With the increased availability of secondary structures in recent years, we update the RAG resource and provide various improvements for analyzing RNA structures.

Description

Our RAG update includes a new supervised clustering algorithm that can suggest RNA motifs that may be "RNA-like". We use this utility to describe RNA motifs as three classes: existing, RNA-like, and non-RNA-like. This produces 126 tree and 16,658 dual graphs as candidate RNA-like topologies using the supervised clustering algorithm with existing RNAs serving as the training data. A comparison of this clustering approach to an earlier method shows considerable improvements. Additional RAG features include greatly expanded search capabilities, an interface to better utilize the benefits of relational database, and improvements to several of the utilities such as directed/labeled graphs and a subgraph search program.

Conclusions

The RAG updates presented here augment the database's intended function - stimulating the search for novel RNA functionality - by classifying available motifs, suggesting new motifs for design, and allowing for more specific searches for specific topologies. The updated RAG web resource offers users a graph-based tool for exploring available RNA motifs and suggesting new RNAs for design.
The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays
Authors: Pinhal Danillo , Yoshimura Tatiana S , Araki Carlos S , Martins Cesar
Published: May 2011

Background

Ribosomal 5S genes are well known for the critical role they play in ribosome folding and functionality. These genes are thought to evolve in a concerted fashion, with high rates of homogenization of gene copies. However, the majority of previous analyses regarding the evolutionary process of rDNA repeats were conducted in invertebrates and plants. Studies have also been conducted on vertebrates, but these analyses were usually restricted to the 18S, 5.8S and 28S rRNA genes. The recent identification of divergent 5S rRNA gene paralogs in the genomes of elasmobranches and teleost fishes indicate that the eukaryotic 5S rRNA gene family has a more complex genomic organization than previously thought. The availability of new sequence data from lower vertebrates such as teleosts and elasmobranches enables an enhanced evolutionary characterization of 5S rDNA among vertebrates.

Results

We identified two variant classes of 5S rDNA sequences in the genomes of Potamotrygonidae stingrays, similar to the genomes of other vertebrates. One class of 5S rRNA genes was shared only by elasmobranches. A broad comparative survey among 100 vertebrate species suggests that the 5S rRNA gene variants in fishes originated from rounds of genome duplication. These variants were then maintained or eliminated by birth-and-death mechanisms, under intense purifying selection. Clustered multiple copies of 5S rDNA variants could have arisen due to unequal crossing over mechanisms. Simultaneously, the distinct genome clusters were independently homogenized, resulting in the maintenance of clusters of highly similar repeats through concerted evolution.

Conclusions

We believe that 5S rDNA molecular evolution in fish genomes is driven by a mixed mechanism that integrates birth-and-death and concerted evolution.
Global analysis of gene expression in response to L-Cysteine deprivation in the anaerobic protozoan parasite Entamoeba histolytica
Authors: Husain Afzal , Jeelani Ghulam , Sato Dan , Nozaki Tomoyoshi
Published: May 2011

Background

Entamoeba histolytica, an enteric protozoan parasite, causes amebic colitis and extra intestinal abscesses in millions of inhabitants of endemic areas. E. histolytica completely lacks glutathione metabolism but possesses L-cysteine as the principle low molecular weight thiol. L-Cysteine is essential for the structure, stability, and various protein functions, including catalysis, electron transfer, redox regulation, nitrogen fixation, and sensing for regulatory processes. Recently, we demonstrated that in E. histolytica, L-cysteine regulates various metabolic pathways including energy, amino acid, and phospholipid metabolism.

Results

In this study, employing custom-made Affymetrix microarrays, we performed time course (3, 6, 12, 24, and 48 h) gene expression analysis upon L-cysteine deprivation. We identified that out of 9,327 genes represented on the array, 290 genes encoding proteins with functions in metabolism, signalling, DNA/RNA regulation, electron transport, stress response, membrane transport, vesicular trafficking/secretion, and cytoskeleton were differentially expressed (≥3 fold) at one or more time points upon L-cysteine deprivation. Approximately 60% of these modulated genes encoded proteins of no known function and annotated as hypothetical proteins. We also attempted further functional analysis of some of the most highly modulated genes by L-cysteine depletion.

Conclusions

To our surprise, L-cysteine depletion caused only limited changes in the expression of genes involved in sulfur-containing amino acid metabolism and oxidative stress defense. In contrast, we observed significant changes in the expression of several genes encoding iron sulfur flavoproteins, a major facilitator super-family transporter, regulator of nonsense transcripts, NADPH-dependent oxido-reductase, short chain dehydrogenase, acetyltransferases, and various other genes involved in diverse cellular functions. This study represents the first genome-wide analysis of transcriptional changes induced by L-cysteine deprivation in protozoan parasites, and in eukaryotic organisms where L-cysteine represents the major intracellular thiol.
Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain
Authors: Gunaratne Preethi H , Lin Ya-Chi , Benham Ashley L , Drnevich Jenny , Coarfa Cristian , Tennakoon Jayantha B , Creighton Chad J , Kim Jong H , Milosavljevic Aleksandar , Watson Michael , Griffiths-Jones Sam , Clayton David F
Published: May 2011

Background

In an important model for neuroscience, songbirds learn to discriminate songs they hear during tape-recorded playbacks, as demonstrated by song-specific habituation of both behavioral and neurogenomic responses in the auditory forebrain. We hypothesized that microRNAs (miRNAs or miRs) may participate in the changing pattern of gene expression induced by song exposure. To test this, we used massively parallel Illumina sequencing to analyse small RNAs from auditory forebrain of adult zebra finches exposed to tape-recorded birdsong or silence.

Results

In the auditory forebrain, we identified 121 known miRNAs conserved in other vertebrates. We also identified 34 novel miRNAs that do not align to human or chicken genomes. Five conserved miRNAs showed significant and consistent changes in copy number after song exposure across three biological replications of the song-silence comparison, with two increasing (tgu-miR-25, tgu-miR-192) and three decreasing (tgu-miR-92, tgu-miR-124, tgu-miR-129-5p). We also detected a locus on the Z sex chromosome that produces three different novel miRNAs, with supporting evidence from Northern blot and TaqMan qPCR assays for differential expression in males and females and in response to song playbacks. One of these, tgu-miR-2954-3p, is predicted (by TargetScan) to regulate eight song-responsive mRNAs that all have functions in cellular proliferation and neuronal differentiation.

Conclusions

The experience of hearing another bird singing alters the profile of miRNAs in the auditory forebrain of zebra finches. The response involves both known conserved miRNAs and novel miRNAs described so far only in the zebra finch, including a novel sex-linked, song-responsive miRNA. These results indicate that miRNAs are likely to contribute to the unique behavioural biology of learned song communication in songbirds.
Study of polymorphisms in tir, eae and tccP2 genes in enterohaemorrhagic and enteropathogenic Escherichia coli of serogroup O26
Authors: Bardiau Marjorie , Labrozzo Sabrina , Mainil Jacques G
Published: May 2011

Background

Enteropathogenic (EPEC) and enterohaemorrhagic (EHEC)Escherichia coliare responsible for food poisoning (enteritis and enterotoxaemia) in humans in developed countries. Cattle are considered to be an important reservoir of EHEC and EPEC strains for humans. Moreover, some of the strains, belonging to the O26, O111, O118 serogroups, for example, are also responsible for digestive disorders in calves. The Translocated intimin receptor (Tir), the intimin (Eae) and the Tir-cytoskeleton coupling protein (TccP) represent three virulence factors implicated in the intimate attachment of the bacteria to the eukaryotic cell. Major variants have already been described for these genes among the different serogroups but minor variations have not often been studied. In this study, we examined the polymorphisms of thetir,eaeandtccP2genes of O26 strains (EPEC and EHEC isolated from bovines and from humans) with the aim to determine whether these polymorphisms are host specific or not.

Results

Of the 70 tested strains, 10 strains (14% of the strains) presented one or several polymorphisms in thetirandeaegenes, which have never previously been described. ConcerningtccP2detection, 47 of the 70 strains (67% of the strains) were found to be positive for this gene. Most of the strains were found to possesstccP2variants described in strains of serogroup O26. Nevertheless, three strains hadtccP2genes respectively described in strains of serogroup O111, O103 and O55. Moreover, none of the polymorphisms was statistically specific to the bovine or the human isolates. Nevertheless, the two major variants oftccP2were statistically associated with the pathotype (EPEC or EHEC).

Conclusions

In conclusion,tirandeaegene polymorphisms were found not to be numerous and not to be predominantly synonymous. Moreover, no difference was observed between human and bovine strains regarding the presence of polymorphisms. Finally, sometccP2variants appeared to be pathotype specific. Further investigations need to be performed on a larger number of strains in order to confirm this specificity.
MDM2 antagonist Nutlin-3a potentiates antitumour activity of cytotoxic drugs in sarcoma cell lines
Authors: Ohnstad Hege O , Paulsen Erik B , Noordhuis Paul , Berg Marianne , Lothe Ragnhild A , Vassilev Lyubomir T , Myklebost Ola
Published: May 2011

Background

Frequent failure and severe side effects of current sarcoma therapy warrants new therapeutic approaches. The small-molecule MDM2 antagonist Nutlin-3a activates the p53 pathway and efficiently induces apoptosis in tumours with amplified MDM2 gene and overexpression of MDM2 protein. However, the majority of human sarcomas have normal level of MDM2 and the therapeutic potential of MDM2 antagonists in this group is still unclear. We have investigated if Nutlin-3a could be employed to augment the response to traditional therapy and/or reduce the genotoxic burden of chemotherapy.

Methods

A panel of sarcoma cell lines with different TP53 and MDM2 status were treated with Nutlin-3a combined with Doxorubicin, Methotrexate or Cisplatin, and their combination index determined.

Results

Clear synergism was observed when Doxorubicin and Nutlin-3a were combined in cell lines with wild-type TP53 and amplified MDM2, or with Methotrexate in both MDM2 normal and amplified sarcoma cell lines, allowing for up to tenfold reduction of cytotoxic drug dose. Interestingly, Nutlin-3a seemed to potentiate the effect of classical drugs as Doxorubicin and Cisplatin in cell lines with mutated TP53, but inhibited the effect of Methotrexate.

Conclusion

The use of Nutlin in combination with classical sarcoma chemotherapy shows promising preclinical potential, but since clear biomarkers are still lacking, clinical trials should be followed up with detailed tumour profiling.
The synthetic peptide P111-136 derived from the C-terminal domain of heparin affin regulatory peptide inhibits tumour growth of prostate cancer PC-3 cells
Authors: Hamma-Kourbali Yamina , Bermek Oya , Bernard-Pierrot Isabelle , Karaky Racha , Martel-Renoir Dominique , Frechault Sophie , Courty José , Delbé Jean
Published: May 2011

Background

Heparin affin regulatory peptide (HARP), also called pleiotrophin, is a heparin-binding, secreted factor that is overexpressed in several tumours and associated to tumour growth, angiogenesis and metastasis. The C-terminus part of HARP composed of amino acids 111 to 136 is particularly involved in its biological activities and we previously established that a synthetic peptide composed of the same amino acids (P111-136) was capable of inhibiting the biological activities of HARP. Here we evaluate the ability of P111-136 to inhibit in vitro and in vivo the growth of a human tumour cell line PC-3 which possess an HARP autocrine loop.

Methods

A total lysate of PC-3 cells was incubated with biotinylated P111-136 and pulled down for the presence of the HARP receptors in Western blot. In vitro, the P111-136 effect on HARP autocrine loop in PC-3 cells was determined by colony formation in soft agar. In vivo, PC-3 cells were inoculated in the flank of athymic nude mice. Animals were treated with P111-136 (5 mg/kg/day) for 25 days. Tumour volume was evaluated during the treatment. After the animal sacrifice, the tumour apoptosis and associated angiogenesis were evaluated by immunohistochemistry. In vivo anti-angiogenic effect was confirmed using a mouse Matrigel™ plug assay.

Results

Using pull down experiments, we identified the HARP receptors RPTPβ/ζ, ALK and nucleolin as P111-136 binding proteins. In vitro, P111-136 inhibits dose-dependently PC-3 cell colony formation. Treatment with P111-136 inhibits significantly the PC-3 tumour growth in the xenograft model as well as tumour angiogenesis. The angiostatic effect of P111-136 on HARP was also confirmed using an in vivo Matrigel™ plug assay in mice

Conclusions

Our results demonstrate that P111-136 strongly inhibits the mitogenic effect of HARP on in vitro and in vivo growth of PC-3 cells. This inhibition could be linked to a direct or indirect binding of this peptide to the HARP receptors (ALK, RPTPβ/ζ, nucleolin). In vivo, the P111-136 treatment significantly inhibits both the PC-3 tumour growth and the associated angiogenesis. Thus, P111-136 may be considered as an interesting pharmacological tool to interfere with tumour growth that has now to be evaluated in other cancer types.
Purification of phage display-modified bacteriophage T4 by affinity chromatography
Authors: Oślizło Anna , Miernikiewicz Paulina , Piotrowicz Agnieszka , Owczarek Barbara , Kopciuch Agnieszka , Figura Grzegorz , Dąbrowska Krystyna
Published: May 2011

Background

Affinity chromatography is one of the most efficient protein purification strategies. This technique comprises a one-step procedure with a purification level in the order of several thousand-fold, adaptable for various proteins, differentiated in their size, shape, charge, and other properties. The aim of this work was to verify the possibility of applying affinity chromatography in bacteriophage purification, with the perspective of therapeutic purposes. T4 is a large, icosahedral phage that may serve as an efficient display platform for foreign peptides or proteins. Here we propose a new method of T4 phage purification by affinity chromatography after its modification with affinity tags (GST and Histag) by in vivo phage display. As any permanent introduction of extraneous DNA into a phage genome is strongly unfavourable for medical purposes, integration of foreign motifs with the phage genome was not applied. The phage was propagated in bacteria expressing fusions of the phage protein Hoc with affinity tags from bacterial plasmids, independently from the phage expression system.

Results

Elution profiles of phages modified with the specific affinity motifs (compared to non-specific phages) document their binding to the affinity resins and effective elution with standard competitive agents. Non-specific binding was also observed, but was 102-105 times weaker than the specific one. GST-modified bacteriophages were also effectively released from glutathione Sepharose by proteolytic cleavage. The possibility of proteolytic release was designed at the stage of expression vector construction. Decrease in LPS content in phage preparations was dependent on the washing intensity; intensive washing resulted in preparations of 11-40 EU/ml.

Conclusions

Affinity tags can be successfully incorporated into the T4 phage capsid by the in vivo phage display technique and they strongly elevate bacteriophage affinity to a specific resin. Affinity chromatography can be considered as a new phage purification method, appropriate for further investigations and development.
Chemical modification of L-glutamine to alpha-amino glutarimide on autoclaving facilitates Agrobacterium infection of host and non-host plants: A new use of a known compound
Authors: Sandal Indra , Bhattacharya Amita , Saini Uksha , Kaur Devinder , Sharma Shveta , Gulati Ashu , Kumar Jonnala K , Kumar Neeraj , Dayma Jyotsna , Das Pralay , Singh Bikram , Ahuja Paramvir S
Published: May 2011

Background

Accidental autoclaving of L-glutamine was found to facilitate theAgrobacteriuminfection of a non host plant like tea in an earlier study. In the present communication, we elucidate the structural changes in L-glutamine due to autoclaving and also confirm the role of heat transformed L-glutamine inAgrobacteriummediated genetic transformation of host/non host plants.

Results

When autoclaved at 121°C and 15 psi for 20 or 40 min, L-glutamine was structurally modified into 5-oxo proline and 3-amino glutarimide (α-amino glutarimide), respectively. Of the two autoclaved products, only α-amino glutarimide facilitatedAgrobacteriuminfection of a number of resistant to susceptible plants. However, the compound did not have anyvirgene inducing property.

Conclusions

We report a one pot autoclave process for the synthesis of 5-oxo proline and α-amino glutarimide from L-glutamine. Xenobiotic detoxifying property of α-amino glutarimide is also proposed.
Regional expression of HOXA4 along the aorta and its potential role in human abdominal aortic aneurysms
Authors: Lillvis John H , Erdman Robert , Schworer Charles M , Golden Alicia , Derr Kimberly , Gatalica Zoran , Cox Laura A , Shen Jianbin , Vander Heide Richard S , Lenk Guy M , Hlavaty Leigh , Li Li , Elmore James R , Franklin David P , Gray John L , Garvin Robert P , Carey David J , Lancaster Wayne D , Tromp Gerard , Kuivaniemi Helena
Published: May 2011

Background

The infrarenal abdominal aorta exhibits increased disease susceptibility relative to other aortic regions. Allograft studies exchanging thoracic and abdominal segments showed that regional susceptibility is maintained regardless of location, suggesting substantial roles for embryological origin, tissue composition and site-specific gene expression.

Results

We analyzed gene expression with microarrays in baboon aortas, and found that members of the HOX gene family exhibited spatial expression differences. HOXA4 was chosen for further study, since it had decreased expression in the abdominal compared to the thoracic aorta. Western blot analysis from 24 human aortas demonstrated significantly higher HOXA4 protein levels in thoracic compared to abdominal tissues (P < 0.001). Immunohistochemical staining for HOXA4 showed nuclear and perinuclear staining in endothelial and smooth muscle cells in aorta. The HOXA4 transcript levels were significantly decreased in human abdominal aortic aneurysms (AAAs) compared to age-matched non-aneurysmal controls (P < 0.00004). Cultured human aortic endothelial and smooth muscle cells stimulated with INF-γ (an important inflammatory cytokine in AAA pathogenesis) showed decreased levels of HOXA4 protein (P < 0.0007).

Conclusions

Our results demonstrated spatial variation in expression of HOXA4 in human aortas that persisted into adulthood and that downregulation of HOXA4 expression was associated with AAAs, an important aortic disease of the ageing population.
A color spectrographic phonocardiography (CSP) applied to the detection and characterization of heart murmurs: preliminary results
Authors: Sarbandi Reza Ramezani , Doyle John D , Navidbakhsh Mahdi , Hassani Kamran , Torabiyan Hassan
Published: May 2011

Background

Although cardiac auscultation remains important to detect abnormal sounds and murmurs indicative of cardiac pathology, the application of electronic methods remains seldom used in everyday clinical practice. In this report we provide preliminary data showing how the phonocardiogram can be analyzed using color spectrographic techniques and discuss how such information may be of future value for noninvasive cardiac monitoring.

Methods

We digitally recorded the phonocardiogram using a high-speed USB interface and the program Gold Wave
http://www.goldwave.com in 55 infants and adults with cardiac structural disease as well as from normal individuals and individuals with innocent murmurs. Color spectrographic analysis of the signal was performed using Spectrogram (Version 16) as a well as custom MATLAB code.

Results

Our preliminary data is presented as a series of seven cases.

Conclusions

We expect the application of spectrographic techniques to phonocardiography to grow substantially as ongoing research demonstrates its utility in various clinical settings. Our evaluation of a simple, low-cost phonocardiographic recording and analysis system to assist in determining the characteristic features of heart murmurs shows promise in helping distinguish innocent systolic murmurs from pathological murmurs in children and is expected to useful in other clinical settings as well.
Histone deacetylase turnover and recovery in sulforaphane-treated colon cancer cells: competing actions of 14-3-3 and Pin1 in HDAC3/SMRT corepressor complex dissociation/reassembly
Authors: Rajendran Praveen , Delage Barbara , Dashwood W Mohaiza , Yu Tian-Wei , Wuth Bradyn , Williams David E , Ho Emily , Dashwood Roderick H
Published: May 2011

Background

Histone deacetylase (HDAC) inhibitors are currently undergoing clinical evaluation as anti-cancer agents. Dietary constituents share certain properties of HDAC inhibitor drugs, including the ability to induce global histone acetylation, turn-on epigenetically-silenced genes, and trigger cell cycle arrest, apoptosis, or differentiation in cancer cells. One such example is sulforaphane (SFN), an isothiocyanate derived from the glucosinolate precursor glucoraphanin, which is abundant in broccoli. Here, we examined the time-course and reversibility of SFN-induced HDAC changes in human colon cancer cells.

Results

Cells underwent progressive G2/M arrest over the period 6-72 h after SFN treatment, during which time HDAC activity increased in the vehicle-treated controls but not in SFN-treated cells. There was a time-dependent loss of class I and selected class II HDAC proteins, with HDAC3 depletion detected ahead of other HDACs. Mechanism studies revealed no apparent effect of calpain, proteasome, protease or caspase inhibitors, but HDAC3 was rescued by cycloheximide or actinomycin D treatment. Among the protein partners implicated in the HDAC3 turnover mechanism, silencing mediator for retinoid and thyroid hormone receptors (SMRT) was phosphorylated in the nucleus within 6 h of SFN treatment, as was HDAC3 itself. Co-immunoprecipitation assays revealed SFN-induced dissociation of HDAC3/SMRT complexes coinciding with increased binding of HDAC3 to 14-3-3 and peptidyl-prolyl cis/trans isomerase 1 (Pin1). Pin1 knockdown blocked the SFN-induced loss of HDAC3. Finally, SFN treatment for 6 or 24 h followed by SFN removal from the culture media led to complete recovery of HDAC activity and HDAC protein expression, during which time cells were released from G2/M arrest.

Conclusion

The current investigation supports a model in which protein kinase CK2 phosphorylates SMRT and HDAC3 in the nucleus, resulting in dissociation of the corepressor complex and enhanced binding of HDAC3 to 14-3-3 or Pin1. In the cytoplasm, release of HDAC3 from 14-3-3 followed by nuclear import is postulated to compete with a Pin1 pathway that directs HDAC3 for degradation. The latter pathway predominates in colon cancer cells exposed continuously to SFN, whereas the former pathway is likely to be favored when SFN has been removed within 24 h, allowing recovery from cell cycle arrest.
Chronic granulomatous disease: a review of the infectious and inflammatory complications
Authors: Song EunKyung , Jaishankar Gayatri Bala , Saleh Hana , Jithpratuck Warit , Sahni Ryan , Krishnaswamy Guha
Published: May 2011

Chronic Granulomatous Disease is the most commonly encountered immunodeficiency involving the phagocyte, and is characterized by repeated infections with bacterial and fungal pathogens, as well as the formation of granulomas in tissue. The disease is the result of a disorder of the NADPH oxidase system, culminating in an inability of the phagocyte to generate superoxide, leading to the defective killing of pathogenic organisms. This can lead to infections withStaphylococcus aureus,Psedomonasspecies,Nocardiaspecies, and fungi (such asAspergillusspecies andCandida albicans). Involvement of vital or large organs can contribute to morbidity and/or mortality in the affected patients. Major advances have occurred in the diagnosis and treatment of this disease, with the potential for gene therapy or stem cell transplantation looming on the horizon.
Proteomic analysis identifies interleukin 11 regulated plasma membrane proteins in human endometrial epithelial cells in vitro
Authors: Yap Joanne , Foo Caroline FH , Lee Ming Yee , Stanton Peter G , Dimitriadis Evdokia
Published: May 2011

Background

During the peri-implantation period, the embryo adheres to an adequately prepared or receptive endometrial surface epithelium. Abnormal embryo adhesion to the endometrium results in embryo implantation failure and infertility. Endometrial epithelial cell plasma membrane proteins critical in regulating adhesion may potentially be infertility biomarkers or targets for treating infertility. Interleukin (IL) 11 regulates human endometrial epithelial cells (hEEC) adhesion. Its production is abnormal in women with infertility. The objective of the study was to identify IL11 regulated plasma membrane proteins in hEEC in vitro using a proteomic approach.

Methods

Using a 2D-differential in-gel electrophoresis (DIGE) electrophoresis combined with LCMS/MS mass spectrometry approach, we identified 20 unique plasma membrane proteins differentially regulated by IL11 in ECC-1 cells, a hEEC derived cell line. Two IL11 regulated proteins with known roles in cell adhesion, annexin A2 (ANXA2) and flotillin-1 (FLOT1), were validated by Western blot and immunocytochemistry in hEEC lines (ECC-1 and an additional cell line, Ishikawa) and primary hEEC. Flotilin-1 was further validated by immunohistochemistry in human endometrium throughout the menstrual cycle (n = 6-8/cycle).

Results

2D-DIGE analysis identified 4 spots that were significantly different between control and IL11 treated group. Of these 4 spots, there were 20 proteins that were identified with LCMS/MS. Two proteins; ANXA2 and FLOT1 were chosen for further analyses and have found to be significantly up-regulated following IL11 treatment. Western blot analysis showed a 2-fold and a 2.5-fold increase of ANXA2 in hEEC membrane fraction of ECC-1 and Ishikawa cells respectively. Similarly, a 1.8-fold and a 2.3/2.4-fold increase was also observed for FLOT1 in hEEC membrane fraction of ECC-1 and Ishikawa cells respectively. In vitro, IL11 induced stronger ANXA2 expression on cell surface of primary hEEC and ECC-1 whilst, the lipid-raft protein FLOT1 demonstrated punctate staining in the apical surface of ECC-1 plasma membranes and was upregulated in the epithelium in the receptive phase of the menstrual cycle (p lower or equal 0.05).

Conclusions

This is the first study to use a proteomics approach to identify hEEC plasma membrane proteins that may be useful as infertility markers or pharmacological targets for fertility regulation.
Cetrorelix suppresses the preovulatory LH surge and ovulation induced by ovulation-inducing factor (OIF) present in llama seminal plasma
Authors: Silva Mauricio E , Smulders Juan P , Guerra Monserrat , Valderrama Ximena P , Letelier Claudia , Adams Gregg P , Ratto Marcelo H
Published: May 2011

Background

The purpose of the study was to determine if the effect of llama OIF on LH secretion is mediated by stimulation of the hypothalamus or pituitary gland.

Methods

Using a 2-by-2 factorial design to examine the effects of OIF vs GnRH with or without a GnRH antagonist, llamas with a growing ovarian follicle greater than or equal to 8 mm were assigned randomly to four groups (n = 7 per group) and a) pre-treated with 1.5 mg of GnRH antagonist (cetrorelix acetate) followed by 1 mg of purified llama OIF, b) pre-treated with 1.5 mg of cetrorelix followed by 50 micrograms of GnRH, c) pre-treated with a placebo (2 ml of saline) followed by 1 mg of purified llama OIF or d) pre-treated with a placebo (2 ml of saline) followed by 50 micrograms of GnRH. Pre-treatment with cetrorelix or saline was given as a single slow intravenous dose 2 hours before intramuscular administration of either GnRH or OIF. Blood samples for LH measurement were taken every 15 minutes from 1.5 hours before to 8 hours after treatment. The ovaries were examined by ultrasonography to detect ovulation and CL formation. Blood samples for progesterone measurement were taken every-other-day from Day 0 (day of treatment) to Day 16.

Results

Ovulation rate was not different (P = 0.89) between placebo+GnRH (86%) and placebo+OIF groups (100%); however, no ovulations were detected in llamas pre-treated with cetrorelix. Plasma LH concentrations surged (P < 0.01) after treatment in both placebo+OIF and placebo+GnRH groups, but not in the cetrorelix groups. Maximum plasma LH concentrations and CL diameter profiles did not differ between the placebo-treated groups, but plasma progesterone concentrations were higher (P < 0.05), on days 6, 8 and 12 after treatment, in the OIF- vs GnRH-treated group.

Conclusion

Cetrorelix (GnRH antagonist) inhibited the preovulatory LH surge induced by OIF in llamas suggesting that LH secretion is modulated by a direct or indirect effect of OIF on GnRH neurons in the hypothalamus.
Induction of Th1Immune responses following laser ablation in a murine model of colorectal liver metastases
Authors: Lin Wen Xu , Fifis Theodora , Malcontenti-Wilson Caterina , Nikfarjam Mehrdad , Muralidharan Vijayaragavan , Nguyen Linh , Christophi Christopher
Published: May 2011

Background

Preliminary experimental studies have suggested that the in situ destruction of tumor tissue by local laser ablation (LA) may also stimulate host immunity against cancer. We investigated local and systemic induction of immune responses after laser ablation in the setting of residual tumor.

Methods

A murine colorectal cancer (CRC) liver metastasis model was used. Selected tumors of liver CRC bearing mice and livers of mice without tumor induction were treated with LA. Liver and tumor tissues from the ablation sites and from distant sites were collected at various time points following LA and changes in CD3+ T cells and Kupffer cells (F4/80 marker) infiltration and the expression of interferon gamma (IFNγ) were investigated by immunohistochemistry and ELISpot. Base line levels of CD3+ T cells and Kupffer cells were established in untreated mice.

Results

The presence of tumor induced significant accumulation of CD3+ T cells and Kupffer cells at the tumor-host interface, within the tumor vascular lakes and increased their baseline concentration within the liver parenchyma. LA of the liver induced accumulation of CD3+ T-cells and Kupffer cells at the site of injury and systemic induction of immune responses as discerned by the presence of IFNγ secreting splenocytes. LA of liver tumors induced significant increase of CD3+ T-cells at site of injury, within normal liver parenchyma, and the tumor-host interface of both ablated and distant tumors. In contrast Kupffer cells only accumulated in ablated tumors and the liver parenchyma but not in distant tumors. IFNγ expression increased significantly in ablated tumors and showed an increasing trend in distant tumors.

Conclusion

Laser ablation in addition to local tumor destruction induces local and systemic Th1 type immune responses which may play a significant role in inhibiting tumor recurrence from residual micrometastases or circulating tumor cells.
Influence of surface properties on the electrical conductivity of silicon nanomembranes
Authors: Zhao Xiangfu , Scott Shelley A , Huang Minghuang , Peng Weina , Kiefer Arnold M , Flack Frank S , Savage Donald E , Lagally Max G
Published: May 2011

Because of the large surface-to-volume ratio, the conductivity of semiconductor nanostructures is very sensitive to surface chemical and structural conditions. Two surface modifications, vacuum hydrogenation (VH) and hydrofluoric acid (HF) cleaning, of silicon nanomembranes (SiNMs) that nominally have the same effect, the hydrogen termination of the surface, are compared. The sheet resistance of the SiNMs, measured by the van der Pauw method, shows that HF etching produces at least an order of magnitude larger drop in sheet resistance than that caused by VH treatment, relative to the very high sheet resistance of samples terminated with native oxide. Re-oxidation rates after these treatments also differ. X-ray photoelectron spectroscopy measurements are consistent with the electrical-conductivity results. We pinpoint the likely cause of the differences.

PACS: 73.63.-b, 62.23.Kn, 73.40.Ty
Photoinduced oxygen release and persistent photoconductivity in ZnO nanowires
Authors: Bao Jiming , Shalish Ilan , Su Zhihua , Gurwitz Ron , Capasso Federico , Wang Xiaowei , Ren Zhifeng
Published: May 2011

Photoconductivity is studied in individual ZnO nanowires. Under ultraviolet (UV) illumination, the induced photocurrents are observed to persist both in air and in vacuum. Their dependence on UV intensity in air is explained by means of photoinduced surface depletion depth decrease caused by oxygen desorption induced by photogenerated holes. The observed photoresponse is much greater in vacuum and proceeds beyond the air photoresponse at a much slower rate of increase. After reaching a maximum, it typically persists indefinitely, as long as good vacuum is maintained. Once vacuum is broken and air is let in, the photocurrent quickly decays down to the typical air-photoresponse values. The extra photoconductivity in vacuum is explained by desorption of adsorbed surface oxygen which is readily pumped out, followed by a further slower desorption of lattice oxygen, resulting in a Zn-rich surface of increased conductivity. The adsorption-desorption balance is fully recovered after the ZnO surface is exposed to air, which suggests that under UV illumination, the ZnO surface is actively "breathing" oxygen, a process that is further enhanced in nanowires by their high surface to volume ratio.
Identification of a functional docking site in the Rpn1 LRR domain for the UBA-UBL domain protein Ddi1
Authors: Gomez Tara A , Kolawa Natalie , Gee Marvin , Sweredoski Michael J , Deshaies Raymond J
Published: May 2011

Background

The proteasome is a multi-subunit protein machine that is the final destination for cellular proteins that have been marked for degradation via an ubiquitin (Ub) chain appendage. These ubiquitylated proteins either bind directly to the intrinsic proteasome ubiqutin chain receptors Rpn10, Rpn13, or Rpt5, or are shuttled to the proteasome by Rad23, Dsk2, or Ddi1. The latter proteins share an Ub association domain (UBA) for binding poly-Ub chains and an Ub-like-domain (UBL) for binding to the proteasome. It has been proposed that shuttling receptors dock on the proteasome via Rpn1, but the precise nature of the docking site remains poorly defined.

Results

To shed light on the recruitment of shuttling receptors to the proteasome, we performed both site-directed mutagenesis and genetic screening to identify mutations in Rpn1 that disrupt its binding to UBA-UBL proteins. Here we demonstrate that delivery of Ub conjugates and docking of Ddi1 (and to a lesser extent Dsk2) to the proteasome are strongly impaired by an aspartic acid to alanine point mutation in the highly-conserved D517 residue of Rpn1. Moreover, degradation of the Ddi1-dependent proteasome substrate, Ufo1, is blocked in rpn1-D517A yeast cells. By contrast, Rad23 recruitment to the proteasome is not affected by rpn1-D517A.

Conclusions

These studies provide insight into the mechanism by which the UBA-UBL protein Ddi1 is recruited to the proteasome to enable Ub-dependent degradation of its ligands. Our studies suggest that different UBA-UBL proteins are recruited to the proteasome by distinct mechanisms.