bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolutionary origin of the Runx/CBFbeta transcription factors – Studies of the most basal metazoans
Authors: Sullivan James C , Sher Daniel , Eisenstein Miriam , Shigesada Katsuya , Reitzel Adam M , Marlow Heather , Levanon Ditsa , Groner Yoram , Finnerty John R , Gat Uri 
Published: August 2008

Abstract

Background
Members of the Runx family of transcriptional regulators, which bind DNA as heterodimers with CBFβ, are known to play critical roles in embryonic development in many triploblastic animals such as mammals and insects. They are known to regulate basic developmental processes such as cell fate determination and cellular potency in multiple stem-cell types, including the sensory nerve cell progenitors of ganglia in mammals.

Results
In this study, we detect and characterize the hitherto unexplored Runx/CBFβ genes of cnidarians and sponges, two basal animal lineages that are well known for their extensive regenerative capacity. Comparative structural modeling indicates that the Runx-CBFβ-DNA complex from most cnidarians and sponges is highly similar to that found in humans, with changes in the residues involved in Runx-CBFβ dimerization in either of the proteins mirrored by compensatory changes in the binding partner. In situ hybridization studies reveal that Nematostella Runx and CBFβ are expressed predominantly in small isolated foci at the base of the ectoderm of the tentacles in adult animals, possibly representing neurons or their progenitors.

Conclusion
These results reveal that Runx and CBFβ likely functioned together to regulate transcription in the common ancestor of all metazoans, and the structure of the Runx-CBFβ-DNA complex has remained extremely conserved since the human-sponge divergence. The expression data suggest a hypothesis that these genes may have played a role in nerve cell differentiation or maintenance in the common ancestor of cnidarians and bilaterians.
Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids
Authors: Hobson Neil , Price Nancy L , Ward Jordan D , Raivio Tracy L 
Published: August 2008

Abstract

Background
Many microbes possess restriction-modification systems that protect them from parasitic DNA molecules. Unfortunately, the presence of a restriction-modification system in a given microbe also hampers genetic analysis. Although plasmids can be successfully conjugated into the enteropathogenic Escherichia coli strain E2348/69 and optimized protocols for competent cell preparation have been developed, we found that a large, low copy (~15) bioluminescent reporter plasmid, pJW15, that we modified for use in EPEC, was exceedingly difficult to transform into E2348/69. We reasoned that a restriction-modification system could be responsible for the low transformation efficiency of E2348/69 and sought to identify and inactivate the responsible gene(s), with the goal of creating an easily transformable strain of EPEC that could complement existing protocols for genetic manipulation of this important pathogen.

Results
Using bioinformatics, we identified genes in the unfinished enteropathogenic Escherichia coli (EPEC) strain E2348/69 genome whose predicted products bear homology to the HsdM methyltransferases, HsdS specificity subunits, and HsdR restriction endonucleases of type I restriction-modification systems. We constructed a strain carrying a deletion of the conserved enzymatic domain of the EPEC HsdR homologue, NH4, and showed that its transformation efficiency was up to four orders of magnitude higher than that of the parent strain. Further, the modification capacity of NH4 remained intact, since plasmids that were normally recalcitrant to transformation into E2348/69 could be transformed upon passage through NH4. NH4 was unaffected in virulence factor production, since bundle forming pilus (BFP) subunits and type III secreted (T3S) proteins were present at equivalent levels to those seen in E2348/69. Further, NH4 was indistinguishable from E2348/69 in tissue culture infection model assays of localized adherence and T3S.

Conclusion
We have shown that EPEC strain E2348/69 utilizes a type I restriction-modification system to limit entry of new DNA. This restriction-modification system does not appear to be involved in virulence determinant expression or infection phenotypes. The hsdR mutant strain should prove useful in genetic analysis of the important diarrheal pathogen EPEC.
A high-throughput and sensitive method to measure Global DNA Methylation: Application in Lung Cancer
Authors: Anisowicz Anthony , Huang Hui , Braunschweiger Karen I , Liu Ziying , Giese Heidi , Wang Huajun , Mamaev Sergey , Olejnik Jerzy , Massion Pierre P , Del Mastro Richard G 
Published: August 2008

Abstract

Background
Genome-wide changes in DNA methylation are an epigenetic phenomenon that can lead to the development of disease. The study of global DNA methylation utilizes technology that requires both expensive equipment and highly specialized skill sets.

Methods
We have designed and developed an assay, CpGlobal, which is easy-to-use, does not utilize PCR, radioactivity and expensive equipment. CpGlobal utilizes methyl-sensitive restriction enzymes, HRP Neutravidin to detect the biotinylated nucleotides incorporated in an end-fill reaction and a luminometer to measure the chemiluminescence. The assay shows high accuracy and reproducibility in measuring global DNA methylation. Furthermore, CpGlobal correlates significantly with High Performance Capillary Electrophoresis (HPCE), a gold standard technology. We have applied the technology to understand the role of global DNA methylation in the natural history of lung cancer. World-wide, it is the leading cause of death attributed to any cancer. The survival rate is 15% over 5 years due to the lack of any clinical symptoms until the disease has progressed to a stage where cure is limited.

Results
Through the use of cell lines and paired normal/tumor samples from patients with non-small cell lung cancer (NSCLC) we show that global DNA hypomethylation is highly associated with the progression of the tumor. In addition, the results provide the first indication that the normal part of the lung from a cancer patient has already experienced a loss of methylation compared to a normal individual.

Conclusion
By detecting these changes in global DNA methylation, CpGlobal may have a role as a barometer for the onset and development of lung cancer.
Modulation of viral replication in macrophages persistently infected with the DA strain of Theiler's murine encephalomyelitis virus
Authors: Steurbaut Stephane , Merckx Ellen , Rombaut Bart , Vrijsen Raf 
Published: August 2008

AbstractBackgroundDemyelinating strains of Theiler's murine encephalomyelitis virus (TMEV) such as the DA strain are the causative agents of a persistent infection that induce a multiple sclerosis-like disease in the central nervous system of susceptible mice. Viral persistence, mainly associated with macrophages, is considered to be an important disease determinant that leads to chronic inflammation, demyelination and autoimmunity. In a previous study, we described the establishment of a persistent DA infection in RAW macrophages, which were therefore named DRAW.ResultsIn the present study we explored the potential of diverse compounds to modulate viral persistence in these DRAW cells. Hemin was found to increase viral yields and to induce cell lysis. Enviroxime and neutralizing anti-TMEV monoclonal antibody were shown to decrease viral yields, whereas interferon-α and interferon-γ completely cleared the persistent infection. We also compared the cytokine pattern secreted by uninfected RAW, DRAW and interferon-cured DRAW macrophages using a cytokine protein array. The chemokine RANTES was markedly upregulated in DRAW cells and restored to a normal expression level after abrogation of the persistent infection with interferon-α or interferon-γ. On the other hand, the chemokine MCP-1 was upregulated in the interferon-cured DRAW cells.ConclusionWe have identified several compounds that modulate viral replication in anin vitromodel system for TMEV persistence. These compounds now await further testing in anin vivosetting to address fundamental questions regarding persistent viral infection and immunopathogenesis.
Survival of Burkholderia pseudomallei in Water
Authors: Moore Richard A , Tuanyok Apichai , Woods Donald E 
Published: August 2008

AbstractBackgroundThe ability ofBurkholderia pseudomalleito survive in water likely contributes to its environmental persistence in endemic regions. To determine the physiological adaptations which allowB. pseudomalleito survive in aqueous environments, we performed microarray analyses ofB. pseudomalleicultures transferred from Luria broth (LB) to distilled water.FindingsIncreased expression of a gene encoding for a putative membrane protein (BPSL0721) was confirmed using alux-based transcriptional reporter system, and maximal expression was noted at approximately 6 hrs after shifting cells from LB to water. A BPSL0721 deficient mutant ofB. pseudomalleiwas able to survive in water for at least 90 days indicating that although involved, BPSL0721 was not essential for survival. BPSL2961, a gene encoding a putative phosphatidylglycerol phosphatase (PGP), was also induced when cells were shifted to water. This gene is likely involved in cell membrane biosynthesis. We were unable to construct a PGP mutant suggesting that the gene is not only involved in survival in water but is essential for cell viability. We also examined mutants of polyhydroxybutyrate synthase (phbC), lipopolysaccharide (LPS) oligosaccharide and capsule synthesis, and these mutations did not affect survival in water. LPS mutants lacking outer core were found to lose viability in water by 200 days indicating that an intact LPS core provides an outer membrane architecture which allows prolonged survival in water.ConclusionThe results from these studies suggest thatB. pseudomalleisurvival in water is a complex process that requires an LPS molecule which contains an intact core region.
Interaction of the growth and tumour suppressor NORE1A with microtubules is not required for its growth-suppressive function
Authors: Moshnikova Anna , Kuznetsov Sergey , Khokhlatchev Andrei V 
Published: August 2008

Abstract

Background
The NORE1 protein was identified in a yeast two-hybrid screen as a Ras effector that binds Ras protein in a GTP-dependent manner. NORE1A is a growth and tumour suppressor that is inactivated in a variety of cancers. In transformed human cells, both full-length NORE1A protein and its effector domain alone (amino acids 191–363) are localized to microtubules and centrosomes. However, the mechanism by which NORE1A associates with these cytoskeletal elements is not known; furthermore, whether centrosomally-associated or microtubule-associated NORE1A suppresses tumour cell growth has not been yet established.

Findings
We have shown that purified NORE1A fails to bind to microtubules in vitro suggesting that other protein(s) mediate NORE1A-microtubule association. Using mass-spectrometry, we identified the Microtubule-Associated Protein 1B (MAP1B) and its homologue C19ORF5 as NORE1A interaction partners. Suppression of C19ORF5 expression by RNA interference (RNAi) and immunodepletion of C19ORF5 protein from cell extracts showed that binding of NORE1A to microtubules is not dependent on C19ORF5. Conversely, RNAi suppression of MAP1B revealed that MAP1B is required for association of NORE1A with microtubules. RNAi-mediated depletion of C19ORF5 or MAP1B did not prevent centrosomal localization of NORE1A. Moreover, the depletion of C19ORF5 or MAP1B did not prevent NORE1A's ability to suppress tumour cell growth.

Conclusion
The interaction of NORE1A with microtubules is mediated by MAP1B, but not C19ORF5 protein. Interaction of NORE1A with centrosomes is not dependent on C19ORF5 or MAP1B, and appears to involve a different mechanism independent of binding to microtubules. The NORE1A microtubular localization is not required for growth suppression.
Analysis of gene expression patterns by microarray hybridization in blood mononuclear cells of SLA-DRB1 defined Canadian Yorkshire pigs
Authors: Nino-Soto Maria I , Jozani Razi Jafari , Bridle Byram , Mallard Bonnie A 
Published: August 2008

AbstractBackgroundThe Swine Leukocyte Antigen (SLA) system encodes molecules for self-nonself discrimination and is associated with immune responses and disease resistance. Three lines of pigs defined by their SLA-DRB1 alleles were developed at the University of Guelph for xenotransplantation and immune response studies. The aim of this project was to explore the potential association between defined SLA-DRB1 alleles and gene transcriptional patterns of other immune-related genes in blood mononuclear cells.FindingsThree SLA-DRB1 alleles were characterized using a RT-PCR-based sequencing method. The loci represented included a new allele, DRB1*04ns01. Next, microarray heterologous (bovine-porcine) hybridization together with qPCR were used to explore differential gene expression between SLA-DRB1-defined groups. Microarray analysis showed significant (p < 0.01) differential expression for 5 genes, mostly related to inflammation. Genes varied according to the comparison analyzed. Further testing with qPCR revealed the same trend of differential expression for 4 of the genes, although statistical significance was reached for only one.ConclusionA new SLA-DRB1 allele was characterized. A potential association was found between SLA-DRB1 alleles and inflammation-related genes. However, the influence of other genes cannot be ruled out. These preliminary findings agree with other studies linking MHC haplotypes and inflammation processes, including autoimmune disease. The study provides an initial view of the biological interactions between the SLA complex and other immune-related genes. Future studies will focus on characterization of SLA-haplotypes associated with these particular alleles and the dynamics of the immune response to antigenic challenges.
Caveolin-1 expression and stress-induced premature senescence in human intervertebral disc degeneration
Authors: Heathfield Sarah Kathleen , Le Maitre Christine Lyn , Hoyland Judith Alison 
Published: August 2008

Abstract
Introduction
Chronic and debilitating low back pain is a common condition and a huge economic burden. Many cases are attributed to age-related degeneration of the intervertebral disc (IVD); however, age-related degeneration appears to occur at an accelerated rate in some individuals. We have previously demonstrated biomarkers of cellular senescence within the human IVD and suggested a role for senescence in IVD degeneration. Senescence occurs with ageing but can also occur prematurely in response to stress. We hypothesised that stress-induced premature senescence (SIPS) occurs within the IVD and here we have investigated the expression and production of caveolin-1, a protein that has been shown previously to be upregulated in SIPS.

Methods
Caveolin-1 gene expression in human nucleus pulposus (NP) cells was assessed by conventional and quantitative real-time polymerase chain reaction (PCR), and caveolin-1 protein expression was examined within human IVDs using immunohistochemistry. The correlation between caveolin-1 and p16INK4a (biomarker of cellular senescence) gene expression was investigated using quantitative real-time PCR.

Results
Caveolin-1 gene expression and protein expression were demonstrated within the human IVD for the first time. NP cells from degenerate discs exhibited elevated levels of caveolin-1 which did not relate to increasing chronological age. A negative correlation was observed between gene expression for caveolin-1 and donor age, and no correlation was found between caveolin-1 protein expression and age. A positive correlation was identified between gene expression of caveolin-1 and p16INK4a.

Conclusion
Our findings are consistent with a role for caveolin-1 in degenerative rather than age-induced changes in the NP. Its expression in IVD tissue and its association with the senescent phenotype suggest that caveolin-1 and SIPS may play a prominent role in the pathogenesis of IVD degeneration.
Proteopedia- a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules
Authors: Hodis Eran , Prilusky Jaime , Martz Eric , Silman Israel , Moult John , Sussman Joel L 
Published: August 2008

AbstractMany scientists lack the background to fully utilize the wealth of solved three-dimensional biomacromolecule structures. Thus, a resource is needed to present structure/function information in a user-friendly manner to a broad scientific audience. Proteopediahttp://www.proteopedia.org is an interactive, wiki web-resource whose pages have embedded three-dimensional structures surrounded by descriptive text containing hyperlinks that change the appearance (view, representations, colors, labels) of the adjacent three-dimensional structure to reflect the concept explained in the text.
The Morbid Psychology of Criminals
Authors: Nicolson David 
Published: August 2008

“Look to the needle of your compass, I beseech you, good Sir Astrophel, and tell us, if yon can, whence comes this storm ?”We now come to the consideration of the last of the three forms of weakmindedness among prisoners, viz., states of mental exaltation. We looked upon the first form, simple mental weakness, as a state of “want of mind,” a negative or irresponsive condition of mind. The second form, states of mental depression, we took as a condition in which there is general inertia of mind with a prominent activity (positive action) in the direction of painful depression.
The Clinical History and Morbid Anatomy of a Case of Anterior Poliomyelitis with Peripheral Nerve Changes. with Illustration
Authors: Bullen F. St. John 
Published: August 2008

R. P., æt. 61; married. Admitted into Wakefield Asylum March, 1885. Formerly labourer in a mill.It was said that patient had been very intemperate, and that his wife and daughter had contracted venereal disease from him. His mother was stated to have been paralytic for several years before death. This is the only instance of family neurosis.
A Study of Forty-four cases of Fever occurring in the Insane
Authors: Keay J. 
Published: August 2008

A case of Acute Mania.—Scarlet Fever.—Recovery.F. M., a domestic servant, aged 20 years, was received into the Inverness Asylum on 13th June, 1894, suffering from acute mania of about a fortnight's duration. There was no assigned cause for the attack, nor was a hereditary tendency to mental or nervous disease admitted.
Medico-Legal Cases
Authors: Mercier  
Published: August 2008

[The Editors request that members will oblige by sending full newspaper reports of all oases of interest as published by the local press at the time of the assises.]Regina v. Kempshall.Catherine Kempshall, 32, of no occupation, was indicted for the wilful murder of Edgar Holland. Prisoner had lived with the deceased as his mistress; had brought an action against him for breach of promise of marriage, which was settled out of Court, the plaintiff to receive £1,000 without costs, to give up all letters and to undertake not to molest the defendant. This agreement the plaintiff subsequently repudiated on the ground that she was not a consenting party. The action was therefore proceeded with, and judgment was given against her in July, 1895. On the result being declared the prisoner had an outburst, which is described by the reporter as one of “positive frenzy,” in which she rushed at the defendant in Court exclaiming, “You beast! pay me! pay me!” and continued to struggle until she was quite exhausted. On the same day she was brought up at the Central Criminal Court for attempting to discharge a pistol at a sister of the defendant, and acquitted. Subsequently she appealed against the result of the trial of the civil action, and her appeal was dismissed. She continued for years a course of annoyance and molestation against the deceased, against his family, and against the solicitors and others who had been concerned in defending him. She broke the windows of a solicitor's office, she assaulted solicitors' clerks, she threatened repeatedly to murder not only the deceased but his solicitors; and she declared that solicitors, counsel, and judges had been bribed by the deceased to defeat the ends of justice and to persecute her. At length she went by appointment to meet the deceased and his solicitor at the office of the former. The deceased promised to provide for her, but remonstrated with her for pretending that he had promised to marry her, upon which she retorted, “You lie, you beast!” and discharged four shots from a revolver at him, inflicting wounds which were ultimately fatal.
The Frequency, Causation, Prevention, and Treatment of Phthisis Pulmonalis in Asylums for the Insane; Essay for which was awarded the Bronze Medal of the Medico-Psychological Association, 1899
Authors: Crookshank F. G. 
Published: August 2008

We are, for obvious reasons, forced to gauge the prevalence of phthisis in asylums by its mortality. Several questions at once present themselves:What is the mortality from phthisis at the present time in the British Islands ? What is the mortality from phthisis in the asylums of the British Islands ?Are these mortalities diminishing or increasing ? And what relation do they bear to one another ?It is easy to propound these questions; it is extremely diffi cult to properly appraise the available data. For, first, if it be desired to compare the mortality from phthisis of asylum inmates with that of the general population, the comparison must be made on the basis of the ratio, in each case, of the annual deaths from phthisis to the average populations in volved. In other words, the phthisis death-rate, and not the percentage of deaths assigned to phthisis, must be estimated.
The Analysis of Dreams [L'Analyse des Rêves]. (L'Année Psychologique, 1909.) Jung, C. J.
Authors: Devine H. 
Published: August 2008

This paper presents clearly and briefly the main principles enunciated by Freud as to the psychology of dreams.The contents of dreams, instead of being the product of accidental and senseless associations, or founded entirely on somatic sensations during sleep, are actually definite products of mental activity and acces sible to a systematic analysis. The organic sensations are not the cause of the dream but only play a secondary rôle, and merely furnish the material for the psychic experience. The dream has its antecedent chains of associations and its own significance like every complex psychic product or volitional act. The apparently obscure and confused images of the dream are the curtains behind which is the essential idea or latent content of the experience. The dream has, therefore, something in dividual conforming to the psychological disposition of the subject, such disposition being itself the result of the previous psychic life.
On the Functions of the Optic Thalamus and the Corpus Striatum
Authors: Blachford Jas. V. 
Published: August 2008

Suggestions have from time to time been made as to the probable functions of the basal ganglia, but so far none of them appear to have been very satisfactory.It seems to be generally accepted that the optic thalami are not merely sensory centres for every or any special kind of sensation, but are large association ganglia, and it is the endeavour here to point out from anatomical, pathological, and other reasons the kind of associations with which they are probably concerned, and the very important part they play in the life of all animals possessing them.