bluuebunny/crossref_metadata_2025_split huggingface dataset:
FastMEDUSA: a parallelized tool to infer gene regulatory networks
Authors: Bozdag Serdar , Li Aiguo , Wuchty Stefan , Fine Howard A. 
Published: June 2010

Abstract
Motivation: In order to construct gene regulatory networks of higher organisms from gene expression and promoter sequence data efficiently, we developed FastMEDUSA. In this parallelized version of the regulatory network-modeling tool MEDUSA, expression and sequence data are shared among a user-defined number of processors on a single multi-core machine or cluster. Our results show that FastMEDUSA allows a more efficient utilization of computational resources. While the determination of a regulatory network of brain tumor in Homo sapiens takes 12 days with MEDUSA, FastMEDUSA obtained the same results in 6 h by utilizing 100 processors.
Availability: Source code and documentation of FastMEDUSA are available at https://wiki.nci.nih.gov/display/NOBbioinf/FastMEDUSA
Contact: hfine@mail.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Treatment of Surfaces with Poly-L-Lysine for Drosophila Cell Cultivation
Authors: Cherbas Lucy , Cherbas Peter 
Published: June 2010

INTRODUCTIONMost commonly used Drosophila cell lines adhere only loosely to the substrate. For some purposes (e.g., time-lapse photography and cytological examination of living cells), it is desirable to fix the growing cells more firmly to the substrate. As described in this protocol, this can be accomplished by treating the substrate with poly-L-lysine, with no obvious detrimental effect on the growth of the cells.
Preparation of Cytoplasmic and Nuclear RNA from Tissue Culture Cells
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W. 
Published: June 2010

INTRODUCTIONIt often is desirable to “prefractionate” RNA before analysis. Ordinarily, this can only be done with tissue culture cells, although it is possible to isolate nuclei and cytoplasm from certain “soft” tissues such as liver and white blood cells. This protocol describes a method for separating nuclei from the cytoplasm that can be used for many tissue culture types. This procedure also is useful for cells grown in suspension or for adherent cells. The procedure relies on swelling in hypotonic buffer, subsequent gentle homogenization, and centrifugation. This method is not appropriate for material (e.g., bacteria, yeast) that has high intrinsic RNase activity, or tissues that are difficult to solubilize, such as muscle tissue or plant material.
Determining the Yield and Quality of Purified RNA
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W. 
Published: June 2010

INTRODUCTIONAfter any RNA purification by any method, it is necessary to ascertain both the amount (yield) and the integrity (quality) of the RNA obtained. This is essential for any subsequent analysis and critical for any comparative analyses. This article discusses several methods for RNA quantitation and provides tips for each.
Nurses’ knowledge and barriers regarding pain management in intensive care units
Authors: Wang Hsiang‐Ling , Tsai Yun‐Fang 
Published: June 2010

Aim.  To explore nurses’ knowledge and barriers regarding pain management in intensive care units.Background.  Pain is a common and treatable condition among intensive care patients. Quality care of these patients depends on the pain knowledge and pain management skills of critical care nurses. However, no single study has explored these nurses’ knowledge of and perceived barriers to pain management in Taiwan.Design.  A cross‐sectional study.Method.  Intensive care unit nurses (n = 370) were recruited from 16 hospitals chosen by stratified sampling across Taipei County in Taiwan. Data were collected on nurses’ knowledge of pain management using the Nurses’ Knowledge and Attitudes Survey‐Taiwanese version, on perceived barriers to pain management using a researcher‐developed scale and on background information.Results.  The overall average correct response rate for the knowledge scale was 53·4%, indicating poor knowledge of pain management. The top barrier to managing pain identified by these nurses was ‘giving proper pain prescription needs doctor’s approval; can’t depend on me’. Knowledge of pain management was significantly and negatively related to perceived barriers to pain management. In addition, scores for knowledge and perceived barriers differed significantly by specific intensive care unit. Knowledge also differed significantly by nurses’ education level, clinical competence level (nursing ladder) and hospital accreditation category.Conclusion.  Our results indicate an urgent need to strengthen pain education by including case analysis for intensive care nurses in Taiwan.Relevance to clinical practice.  Pain education should target knowledge deficits and barriers to changing pain management approaches for Taiwanese nurses in intensive care units.
The crystal structures of two salivary cystatins from the tick Ixodes scapularis and the effect of these inhibitors on the establishment of Borrelia burgdorferi infection in a murine model
Authors: Kotsyfakis Michalis , Horka Helena , Salat Jiri , Andersen John F. 
Published: June 2010

SummaryWe have previously demonstrated that two salivary cysteine protease inhibitors from the Borrelia burgdorferi (Lyme disease) vector Ixodes scapularis– namely sialostatins L and L2 – play an important role in tick biology, as demonstrated by the fact that silencing of both sialostatins in tandem results in severe feeding defects. Here we show that sialostatin L2 – but not sialostatin L – facilitates the growth of B. burgdorferi in murine skin. To examine the structural basis underlying these differential effects of the two sialostatins, we have determined the crystal structures of both sialostatin L and L2. This is the first structural analysis of cystatins from an invertebrate source. Sialostatin L2 crystallizes as a monomer with an ‘unusual’ conformation of the N‐terminus, while sialostatin L crystallizes as a domain‐swapped dimer with an N‐terminal conformation similar to other cystatins. Deletion of the ‘unusual’ N‐terminal five residues of sialostatin L2 results in marked changes in its selectivity, suggesting that this region is a particularly important determinant of the biochemical activity of sialostatin L2. Collectively, our results reveal the structure of two tick salivary components that facilitate vector blood feeding and that one of them also supports pathogen transmission to the vertebrate host.
Screening Leishmania donovani‐specific genes required for visceral infection
Authors: Zhang Wen‐Wei , Matlashewski Greg 
Published: June 2010

SummaryComparison of the Leishmania infantum genome with Leishmania braziliensis and Leishmania major genomes has identified 25 L. infantum species‐specific genes that are absent or pseudogenes in L. major and L. braziliensis. To determine whether these L. infantum species‐specific genes are involved in visceral Leishmania infection, we cloned the orthologues of 14 L. infantum species‐specific genes from the genetically closely related Leishmania donovani and introduced them into L. major. Two of these L. donovani species‐specific genes were found to significantly increase L. major survival in visceral organs in BALB/c mice. One (orthologue of LinJ28_V3.0340; Ld2834) of these two genes was further investigated. The L. donovani Ld2834 null mutants displayed dramatically reduced virulence in BALB/c mice and were unable to survive in axenic amastigote culture conditions arguing that Ld2834 plays a crucial role in enabling L. donovani survive at the increased temperature typically associated with visceral organs. Ld2834 encodes a 50 kDa protein that is localized in the cytoplasma and has no significant sequence similarity with other known genes. This study validates the importance of comparative genomics for understanding Leishmania species pathology and argues that Leishmania species‐specific genes play important roles in tissue tropism and virulence.
M. tuberculosis intramembrane protease Rip1 controls transcription through three anti‐sigma factor substrates
Authors: Sklar Joseph G. , Makinoshima Hideki , Schneider Jessica S. , Glickman Michael S. 
Published: June 2010

SummaryRegulated intramembrane proteolysis (RIP) is a mechanism of transmembrane signal transduction that functions through intramembrane proteolysis of substrates. We previously reported that the RIP metalloprotease Rv2869c (Rip1) is a determinant of Mycobacterium tuberculosis (Mtb) cell envelope composition and virulence, but the substrates of Rip1 were undefined. Here we show that Rip1 cleaves three transmembrane anti‐sigma factors: anti‐SigK, anti‐SigL and anti‐SigM, negative regulators of Sigma K, L and M. We show that transcriptional activation of katG in response to phenanthroline requires activation of SigK and SigL by Rip1 cleavage of anti‐SigK and anti‐SigL. We also demonstrate a Rip1‐dependent pathway that activates the genes for the mycolic acid biosynthetic enzyme KasA and the resuscitation promoting factor RpfC, but represses the bacterioferritin encoding gene bfrB. Regulation of these three genes by Rip1 is not reproduced by deletion of Sigma K, L or M, either indicating a requirement for multiple Rip1 substrates or additional arms of the Rip1 pathway. These results identify a branched proteolytic signal transduction system in which a single intramembrane protease cleaves three anti‐sigma factor substrates to control multiple downstream pathways involved in lipid biosynthesis and defence against oxidative stress.
The high affinity iron permease is a key virulence factor required forRhizopus oryzaepathogenesis
Authors: Ibrahim Ashraf S. , Gebremariam Teclegiorgis , Lin Lin , Luo Guanpingsheng , Husseiny Mohamed I. , Skory Christopher D. , Fu Yue , French Samuel W. , Edwards, Jr John E. , Spellberg Brad 
Published: June 2010

SummaryRhizopus oryzaeis the most common cause of mucormycosis, an angioinvasive fungal infection that causes more then 50% mortality rate despite first‐line therapy. Clinical and animal model data clearly demonstrate that the presence of elevated available serum iron predisposes the host to mucormycosis. The high affinity iron permease gene (FTR1) is required forR. oryzaeiron transport in iron‐depleted environments. Here we demonstrate thatFTR1is required for full virulence ofR. oryzaein mice. We show thatFTR1is expressed during infection in diabetic ketoacidosis (DKA) mice. In addition, we disruptedFTR1by double cross‐over homologous recombination, but multinucleatedR. oryzaecould not be forced to segregate to a homokaryotic null allele. Nevertheless, a reduction of the relative copy number ofFTR1and inhibition ofFTR1expression by RNAi compromised the ability ofR. oryzaeto acquire ironin vitroand reduced its virulence in DKA mice. Importantly, passive immunization with anti‐Ftr1p immune sera protected DKA mice from infection withR. oryzae. Thus,FTR1is a virulence factor forR. oryzae, and anti‐Ftr1p passive immunotherapy deserves further evaluation as a strategy to improve outcomes of deadly mucormycosis.
The inducer maltotriose binds in the central cavity of the tetratricopeptide‐like sensor domain of MalT, a bacterial STAND transcription factor
Authors: Danot Olivier 
Published: June 2010

SummarySignal transduction ATPases with numerous domains (STAND) are sophisticated proteins that integrate several signals and respond by building multimeric platforms allowing signalling in various processes: apoptosis, innate immunity, bacterial metabolism. They comprise a conserved nucleotide oligomerization domain (NOD), which functions as a binary switch that oscillates between the OFF (ADP‐bound) and the ON (ATP‐bound) conformation, and non conserved sensor and effector domains. Transition from the OFF form to the ON form strictly depends on the binding of an inducer to the sensor domain. The interaction of the inducer with this domain was studied in MalT, a model STAND protein. MalT sensor domain has a SUPR (superhelical repeats) fold resembling a cylinder with a central cavity. The cavity was subjected to an alanine‐scanning approach, and the effects of the alanine substitutions on inducer binding and transcription activation were analyzed. This work unambiguously showed that the inducer maltotriose binds inside the cavity, and a patch on the inner surface was proposed to be the primary maltotriose binding‐site. Furthermore, limited proteolysis suggested that maltotriose binding changes the conformation of the sensor domain.
The mycobacteriophage Ms6 encodes a chaperone‐like protein involved in the endolysin delivery to the peptidoglycan
Authors: Catalão Maria João , Gil Filipa , Moniz‐Pereira José , Pimentel Madalena 
Published: June 2010

SummaryLike most double‐stranded (ds) DNA phages, mycobacteriophage Ms6 uses the holin‐endolysin system to achieve lysis of its host. In addition to endolysin (lysA) and holin (hol) genes, Ms6 encodes three accessory lysis proteins. In this study we investigated the lysis function of Gp1, which is encoded by the gp1 gene that lies immediately upstream of lysA. Escherichia coli lysis was observed after coexpression of LysA and Gp1 in the absence of Ms6 holin. Gp1 does not belong to the holin class of proteins, and we provide evidence that it shares several characteristics with molecular chaperones. We show that Gp1 interacts with LysA, and that this interaction is necessary for LysA delivery to its target. In addition, PhoA fusions showed that, in Mycobacterium smegmatis, LysA is exported to the extracytoplasmic environment in the presence of Gp1. We also show that Gp1 is necessary for efficient M. smegmatis lysis, as Ms6 gp1 deletion results in host lysis defects. We propose that delivery of Ms6 endolysin to the murein layer is assisted by Gp1, a chaperone‐like protein, in a holin‐independent manner.
Guanosine 5′‐diphosphate 3′‐diphosphate (ppGpp) as a negative modulator of polynucleotide phosphorylase activity in a ‘rare’ actinomycete
Authors: Siculella Luisa , Damiano Fabrizio , Di Summa Roberta , Tredici Salvatore M. , Alduina Rosa , Gnoni Gabriele V. , Alifano Pietro 
Published: June 2010

SummaryWith the beginning of the idiophase the highly phosphorylated guanylic nucleotides guanosine 5′‐diphosphate 3′‐diphosphate (ppGpp) and guanosine 5′‐triphosphate 3′‐diphosphate (pppGpp), collectively referred to as (p)ppGpp, activate stress survival adaptation programmes and trigger secondary metabolism in actinomycetes. The major target of (p)ppGpp is the RNA polymerase, where it binds altering the enzyme activity. In this study analysis of the polynucleotide phosphorylase (PNPase)‐encoding gene pnp mRNA, in Nonomuraea sp. ATCC 39727 wild‐type, constitutively stringent and relaxed strains, led us to hypothesize that in actinomycetes (p)ppGpp may modulate gene expression at the level of RNA decay also. This hypothesis was supported by: (i) in vitro evidence that ppGpp, at physiological levels, inhibited both polynucleotide polymerase and phosphorolytic activities of PNPase in Nonomuraea sp., but not in Escherichia coli, (ii) in vivo data showing that the pnp mRNA and the A40926 antibiotic cluster‐specific dpgA mRNA were stabilized during the idiophase in the wild‐type strain but not in a relaxed mutant and (iii) measurement of chemical decay of pulse‐labelled bulk mRNA. The results of biochemical tests suggest competitive inhibition of ppGpp with respect to nucleoside diphosphates in polynucleotide polymerase assays and mixed inhibition with respect to inorganic phosphate when the RNA phosphorolytic activity was determined.
Raman microspectroscopy reveals long‐term extracellular activity of chlamydiae
Authors: Haider Susanne , Wagner Michael , Schmid Markus C. , Sixt Barbara S. , Christian Jan G. , Häcker Georg , Pichler Peter , Mechtler Karl , Müller Albert , Baranyi Christian , Toenshoff Elena R. , Montanaro Jacqueline , Horn Matthias 
Published: June 2010

SummaryThe phylum Chlamydiae consists exclusively of obligate intracellular bacteria. Some of them are formidable pathogens of humans, while others occur as symbionts of amoebae. These genetically intractable bacteria possess a developmental cycle consisting of replicative reticulate bodies and infectious elementary bodies, which are believed to be physiologically inactive. Confocal Raman microspectroscopy was applied to differentiate between reticulate bodies and elementary bodies of Protochlamydia amoebophila and to demonstrate in situ the labelling of this amoeba symbiont after addition of isotope‐labelled phenylalanine. Unexpectedly, uptake of this amino acid was also observed for both developmental stages for up to 3 weeks, if incubated extracellularly with labelled phenylalanine, and P. amoebophila remained infective during this period. Furthermore, P. amoebophila energizes its membrane and performs protein synthesis outside of its host. Importantly, amino acid uptake and protein synthesis after extended extracellular incubation could also be demonstrated for the human pathogen Chlamydia trachomatis, which synthesizes stress‐related proteins under these conditions as shown by 2‐D gel electrophoresis and MALDI‐TOF/TOF mass spectrometry. These findings change our perception of chlamydial biology and reveal that host‐free analyses possess a previously not recognized potential for direct experimental access to these elusive microorganisms.
Vibrio cholerae El Tor TcpA crystal structure and mechanism for pilus‐mediated microcolony formation
Authors: Lim Mindy S. , Ng Dixon , Zong ZuSheng , Arvai Andrew S. , Taylor Ronald K. , Tainer John A. , Craig Lisa 
Published: June 2010

SummaryType IV pili (T4P) are critical to virulence for Vibrio cholerae and other bacterial pathogens. Among their diverse functions, T4P mediate microcolony formation, which protects the bacteria from host defences and concentrates secreted toxins. The T4P of the two V. cholerae O1 disease biotypes, classical and El Tor, share 81% identity in their TcpA subunits, yet these filaments differ in their interaction patterns as assessed by electron microscopy. To understand the molecular basis for pilus‐mediated microcolony formation, we solved a 1.5 Å resolution crystal structure of N‐terminally truncated El Tor TcpA and compared it with that of classical TcpA. Residues that differ between the two pilins are located on surface‐exposed regions of the TcpA subunits. By iteratively changing these non‐conserved amino acids in classical TcpA to their respective residues in El Tor TcpA, we identified residues that profoundly affect pilus:pilus interaction patterns and bacterial aggregation. These residues lie on either the protruding d‐region of the TcpA subunit or in a cavity between pilin subunits in the pilus filament. Our results support a model whereby pili interact via intercalation of surface protrusions on one filament into depressions between subunits on adjacent filaments as a means to hold V. cholerae cells together in microcolonies.
‘Munchausen syndrome by proxy’ presenting as battered child syndrome: a report of two cases
Authors: Sugandhan Selvendran , Gupta Somesh , Khandpur Sujay , Khanna Neena , Mehta Manju , Inna Prashanth 
Published: June 2010

AbstractBackground  Child abuse is a major public health crisis and is on the rise. Dermatologists are frequently involved in its evaluation in differentiating abusive injuries from accidental injuries and in excluding pathological conditions that may mimic abuse. Battered child syndrome or physical abuse is not only a common form of child abuse but can also result from a rarer form of child abuse known as Munchausen syndrome by proxy. In this form of abuse, mother, who is the usual perpetrator, induces an illness or abuses the child for her own self‐serving psychological needs.Methods  We report two cases of battered child syndrome. In both the cases, Psychiatric evaluation was performed on both parents. Observation through one‐way mirror was done with the mother and the child alone. Routine hematological and biochemical investigations were done.Results  Diagnosis of Munchausen syndrome by proxy was firmly established in one case and was considered as a possibility in the other.Conclusion  A multidisciplinary team effort is essential in evaluating such cases, and dermatologists should be aware and be well informed about this condition that can be potentially lethal but easily overlooked.
Enteric‐coated mycophenolate sodium in the treatment of refractory pemphigus
Authors: Bongiorno Maria Rita , Pistone Giuseppe , Doukaki Spyridoula , Aricò Mario 
Published: June 2010

AbstractBackground One of the major goals of pemphigus therapy is to reduce the patient’s cumulative exposure to systemic corticosteroids. To investigate the efficacy of enteric‐coated mycophenolate sodium (EC‐MPS), 10 patients with active, refractory pemphigus vulgaris (PV) or foliaceous (PF) were treated with EC‐MPS (1440 mg daily) and prednisone (75 mg daily) over 18 months.Observations Following EC‐MPS/prednisone therapy, disease progression was inhibited between days 30 and 45 in 9/10 patients (8 PV; 1 PF). At 18 months, 8/9 PV patients had clinically quiescent disease; EC‐MPS therapy was no longer required in two patients as a result of disease remission. The remaining PV patient showed no response to treatment. The PF patient also had clinically quiescent disease but with high levels of anti‐desmoglein‐1. ECMPS dose was reduced to 720 mg daily in 4/9 patients by month 6. Average daily prednisone requirement decreased to 25 mg at 6 months and to 15 mg at 18 months. Three adverse events were reported: headache (two cases; one mild and one moderate) and significant increase in blood glucose (one case; moderate).Conclusions Enteric‐coated mycophenolate sodium is effective and safe as an adjuvant therapy in patients with refractory pemphigus and may be effective even in patients whose disease is unresponsive to azathioprine.
Is psoriasis a pre‐atherosclerotic disease? Increased insulin resistance and impaired endothelial function in patients with psoriasis
Authors: Karadag Ayse Serap , Yavuz Bunyamin , Ertugrul Derun Taner , Akin Kadir Okhan , Yalcin Ahmet Arif , Deveci Onur Sinan , Ata Naim , Kucukazman Metin , Dal Kursad 
Published: June 2010

AbstractBackground  Several studies have shown an association between psoriasis and atherosclerotic risk factors. In this study, we aimed to evaluate endothelial function by flow‐mediated dilation (FMD) and insulin resistance by Homeostasis model assessment‐insulin resistance (HOMA‐IR).Methods  We examined 75 consecutive psoriasis patients and 50 healthy controls. All subjects underwent transthoracic echocardiography and brachial artery imaging for detecting FMD. Fasting blood samples were drawn from all subjects for measuring insulin, C‐peptide, fasting blood glucose. HOMA‐IR was calculated.Results  Baseline characteristics of both groups were similar. Twenty‐four psoriatic patients had arthritis. Insulin [9.3 (4.0–208.1) vs. 8.2 (2.3–16.5) mcIU/ml, P = 0.016] and C‐peptide [2.5 (0.9–20.0) vs. 2.0 (0.9–3.7) ng/ml, P = 0.009] levels were significantly higher in patients with psoriasis than in controls. HOMA‐IR [2.1 (0.8–68.9) vs. 1.8 (0.6–8.6), P = 0.036] was significantly higher in patients with psoriasis than in controls. FMD was reduced in patients with psoriasis compared with healthy controls (5.6 ± 1.9% vs. 10.9 ± 1.9%, P < 0.001).Conclusions  This study demonstrated a significant impairment in endothelial function and increased insulin resistance in patients with psoriasis. This is a comprehensive study for identifying atherosclerotic risk factors in psoriasis. We suggest that psoriatic patients should be paid attention for atherosclerosis and its risk factors.