bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into organ-specific pathogen defense responses in plants: RNA-seq analysis of potato tuber-Phytophthora infestans interactions
Authors: Gao Liangliang , Tu Zheng Jin , Millett Benjamin P , Bradeen James M 
Published: May 2013

AbstractBackgroundThe late blight pathogenPhytophthora infestanscan attack both potato foliage and tubers. Although interaction transcriptome dynamics between potato foliage and various pathogens have been reported, no transcriptome study has focused specifically upon how potato tubers respond to pathogen infection. When inoculated withP. infestans, tubers of nontransformed ‘Russet Burbank’ (WT) potato develop late blight disease while those of transgenic ‘Russet Burbank’ line SP2211 (+RB), which expresses the potato late blight resistance geneRB(Rpi-blb1), do not. We compared transcriptome responses toP. infestansinoculation in tubers of these two lines.ResultsWe demonstrated the practicality of RNA-seq to study tetraploid potato and present the first RNA-seq study of potato tuber diseases. A total of 483 million paired end Illumina RNA-seq reads were generated, representing the transcription of around 30,000 potato genes. Differentially expressed genes, gene groups and ontology bins that exhibited differences between the WT and+RBlines were identified.P. infestanstranscripts, including those of known effectors, were also identified.ConclusionFaster and stronger activation of defense related genes, gene groups and ontology bins correlate with successful tuber resistance againstP. infestans. Our results suggest that the hypersensitive response is likely a general form of resistance against the hemibiotrophicP. infestans—even in potato tubers, organs that develop below ground.
LMNA mutations in Polish patients with dilated cardiomyopathy: prevalence, clinical characteristics, and in vitro studies
Authors: Saj Michal , Bilinska Zofia T , Tarnowska Agnieszka , Sioma Agnieszka , Bolongo Pierrette , Sobieszczanska-Malek Malgorzata , Michalak Ewa , Golen Dorota , Mazurkiewicz Lukasz , Malek Lukasz , Walczak Ewa , Fidzianska Anna , Grzybowski Jacek , Przybylski Andrzej , Zielinski Tomasz , Korewicki Jerzy , Tesson Frederique , Ploski Rafal 
Published: May 2013

Abstract

Background

LMNA mutations are most frequently involved in the pathogenesis of dilated cardiomyopathy with conduction disease. The goal of this study was to identify LMNA mutations, estimate their frequency among Polish dilated cardiomyopathy patients and characterize their effect both in vivo and in vitro.

Methods
Between January, 2008 and June, 2012 two patient populations were screened for the presence of LMNA mutations by direct sequencing: 66 dilated cardiomyopathy patients including 27 heart transplant recipients and 39 dilated cardiomyopathy patients with heart failure referred for heart transplantation evaluation, and 44 consecutive dilated cardiomyopathy patients, referred for a family evaluation and mutation screening.

Results
We detected nine non-synonymous mutations including three novel mutations: p.Ser431*, p.Val256Gly and p.Gly400Argfs*11 deletion. There were 25 carriers altogether in nine families. The carriers were mostly characterized by dilated cardiomyopathy and heart failure with conduction system disease and/or complex ventricular arrhythmia, although five were asymptomatic. Among the LMNA mutation carriers, six underwent heart transplantation, fourteen ICD implantation and eight had pacemaker. In addition, we obtained ultrastructural images of cardiomyocytes from the patient carrying p.Thr510Tyrfs*42. Furthermore, because the novel p.Val256Gly mutation was found in a sporadic case, we verified its pathogenicity by expressing the mutation in a cellular model.

Conclusions
In conclusion, in the two referral centre populations, the screening revealed five mutations among 66 heart transplant recipients or patients referred for heart transplantation (7.6%) and four mutations among 44 consecutive dilated cardiomyopathy patients referred for familial evaluation (9.1%). Dilated cardiomyopathy patients with LMNA mutations have poor prognosis, however considerable clinical variability is present among family members.
Calcium and vitamin D intakes in children: a randomized controlled trial
Authors: Cosenza Linda , Pezzella Vincenza , Nocerino Rita , Di Costanzo Margherita , Coruzzo Anna , Passariello Annalisa , Leone Ludovica , Savoia Marcella , Del Puente Antonio , Esposito Antonella , Terrin Gianluca , Berni Canani Roberto 
Published: May 2013

Abstract

Background
Calcium (Ca2+) and vitamin D (VitD) play an important role in child health. We evaluated the daily intake of Ca2+ and VitD in healthy children. Moreover, we demonstrate the efficacy of Ca2+ and VitD supplementation.

Methods
Daily Ca2 + and VitD intake was evaluated in consecutive healthy children through a validated questionnaire. Subjects with <70% of dietary reference intakes (DRIs) of Ca2+ and VitD were invited to participate in a prospective randomized trial with 2 groups of nutritional intervention: Group 1, dietary counseling aiming to optimize daily Ca2+ and VitD intake plus administration of a commercially available Ca2 + and VitD supplementation product; Group 2, dietary counseling alone. At the enrollment (T0) and after 4 months (T1) serum 25(OH) Vitamin D levels were assessed.

Results
We evaluated 150 healthy children (male 50%, mean age 10 years); at baseline a low VitD intake was observed in all subjects (median 0.79 μg/die, IQR 1.78; range 0.01-5.02); this condition was associated with Ca2+ intake <70% of the DRIs in 82 subjects (55%). At baseline serum 25(OH)D levels were low (<30 ng/ml) in all study subjects and after 4 months of nutritional intervention, a normalization of serum 25(OH)D levels (≥30 ng/ml) was observed in all children in Group 1 and in only one subject in Group 2 [Group 1: T1 33.8 ng/ml (IQR 2.5) vs Group 2: T1 24.5 ng/ml (IQR 5.2), p <0.001].

Conclusions
Adequate Ca2+ and VitD intakes are difficult to obtain through dietary counseling alone in pediatric subjects. Oral supplementation with of Ca2+ and VitD is a reliable strategy to prevent this condition.

Trial registration
The study was registered in Clinical Trials Protocol Registration System (ID number: NCT01638494).
Expression level of the growth factor progranulin is related with development of systemic lupus erythematosus
Authors: Qiu Feng , Song Lijun , Ding Feng , Liu Huaxiang , Shu Qiang , Yang Ning , Liu Weiwei , Li Xingfu 
Published: May 2013

AbstractBackgroundThis study is to investigate the expression of progranulin (PGRN) in systemic lupus erythematosus (SLE) patients and the effect of glucocorticoid (GC) treatment on its expression.MethodsThirty newly diagnosed severe SLE patients and 30 healthy subjects were enrolled in this study. The serum levels of PGRN and the inflammatory factors of SLE were detected by ELISA and the mRNA expression of these proteins were detected by real-time PCR.ResultsThe serum levels of PGRN, IL-6, PR3, TNFR, TNF-α and anti-dsDNA antibody in SLE patients were increased significantly compared with healthy controls (P < 0.05). The relative expression of PGRN mRNA was increased by 4.88-fold in pre-treatment SLE patients compared with controls (P < 0.05). After prednisone treatment, the serum levels of PGRN decreased significantly, and the relative expression of PGRN mRNA was decreased by 1.34-fold compared with the untreated controls (P < 0.01). Moreover, Serum concentration of PGRN was correlated with serum levels of IL-6, TNF-α, TNFR and anti-dsDNA antibody in both pre-treatment and post-treatment SLE patients.ConclusionsPGRN is up-regulated in the SLE patients and is correlated with pro-inflammatory cytokines and anti-dsDNA antibody. Glucocorticoids can down-regulate the expression of PGRN in SLE patients.Virtual slideshttp://www.diagnosticpathology.diagnomx.eu/vs/1562484036905973
RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing
Authors: Cushing Anna , Flaherty Patrick , Hopmans Erik , Bell John M , Ji Hanlee P 
Published: May 2013

Abstract

Background
Rare single nucleotide variants play an important role in genetic diversity and heterogeneity of specific human disease. For example, an individual clinical sample can harbor rare mutations at minor frequencies. Genetic diversity within an individual clinical sample is oftentimes reflected in rare mutations. Therefore, detecting rare variants prior to treatment may prove to be a useful predictor for therapeutic response. Current rare variant detection algorithms using next generation DNA sequencing are limited by inherent sequencing error rate and platform availability.

Findings
Here we describe an optimized implementation of a rare variant detection algorithm called RVD for use in targeted gene resequencing. RVD is available both as a command-line program and for use in MATLAB and estimates context-specific error using a beta-binomial model to call variants with minor allele frequency (MAF) as low as 0.1%. We show that RVD accepts standard BAM formatted sequence files. We tested RVD analysis on multiple Illumina sequencing platforms, among the most widely used DNA sequencing platforms.

Conclusions
RVD meets a growing need for highly sensitive and specific tools for variant detection. To demonstrate the usefulness of RVD, we carried out a thorough analysis of the software’s performance on synthetic and clinical virus samples sequenced on both an Illumina GAIIx and a MiSeq. We expect RVD can improve understanding the genetics and treatment of common viral diseases including influenza. RVD is available at the following URL:http://dna-discovery.stanford.edu/software/rvd/.
Cytotoxic activities of phytochemicals from Ferula species
Authors: Valiahdi Seied Mojtaba , Iranshahi Mehrdad , Sahebkar Amirhossein 
Published: May 2013

Abstract

Background

Ferula species are reputed in folk medicine for the treatment of a variety of disorders. There have been sporadic reports on the chemopreventive and chemosensitizing activities of some terpenoid coumarin derivatives from the genus Ferula. The present study investigated the cytotoxic activity of 11 phytochemicals (conferone, farnesiferol A, acantrifoside E, mogoltadone, diversin, galbanic acid, herniarin, 7-isopentenyloxycoumarin, umbelliprenin, stylosin and tschimgine) from Ferula species together with a newly synthesized prenylated derivative of curcumin (gercumin II).

Methods
Cytotoxic activity of phytochemicals was evaluated against ovarian carcinoma (CH1), lung cancer (A549) and melanoma (SK-MEL-28) cell lines using MTT assay.

Results and conclusion
Overall, moderate cytotoxic activity was observed from the tested compounds with IC50 values in the micromolar range. The highest activity against CH1 and A549 lines was from conferone while stylosin and tschimgine were the most potent compounds against SK-MEL-28 line. In conclusion, the findings of the present investigation did not support a potent cytotoxic activity of the tested phytochemicals against CH1, A549 and SK-MEL-28 cell lines. With respect to previous reports, the beneficial impact of these phytochemicals in cancer therapy may be more attributable to their chemopreventive or chemosensitizing activity rather than direct cytotoxic effects.
The Molecular Biology of Nucleotide Excision Repair of DNA: Recent Progress
Authors: Friedberg Errol C. 
Published: May 2013

ABSTRACT
Recent years have witnessed significant progress towards understanding the molecular mechanism of nucleotide excision repair in living cells. Biochemical studies in Escherichia coli, and genetic and molecular studies in lower and higher eukaryotes have revealed an unexpected complexity suggesting interesting protein-protein and protein-DNA interactions. This review considers selected aspects of nucleotide excision repair in E. coli, Saccharomyces cerevisiae and mammalian cells, with a particular emphasis on new observations and on models that may provide explanations for the complexity evident from genetic and biochemical studies.
Molecular Evidence for Cleavage of Intradimer Phosphodiester Linkage as a Novel Step in Excision Repair of Cyclobutyl Pyrimidine Photodimers in Cultured Human Cells
Authors: Paterson M. C. , Middlestadt M. V. , Macfarlane S. J. , Gentner N. E. , Weinfeld M. , Eker A. P. M. 
Published: May 2013

ABSTRACT
A re-analysis of the metabolic fate of ultraviolet light (u.v.)-induced cyclobutyl pyrimidine dimers in the DNA of dermal fibroblasts from patients with different genetic forms of xeroderma pigmentosum (XP), a rare cancer-prone skin disorder, has provided new insight into the mode of dimer repair in normal human cells. When DNA isolated from post-u.v. incubated cultures was subjected to enzymic photoreactivation (PR) to probe dimer authenticity, single-strand scissions were produced in the damaged DNA of incubated XP group A and D cells, but not in DNA from XP group C cells or normal controls. Since enzymic PR treatment ruptures only the cyclobutane ring, these results suggested that in dimer excision-defective XP group A and D strains, the intradimer phosphodiester bond may have been cleaved without site restoration. Such a cleavage event had not previously been detected; the possibility that this reaction may be an early step in the normal excision-repair process is supported by the observed release of free thymidine (dThd) and its monophosphate (TMP), but not of thymine, upon photochemical reversal of the dimercontaining excision fragments isolated from post-u.v. incubated normal cells. The combined number of dThd and TMP molecules released was equal to ≈ 80% of the number of dimers photoreversed; for such release to occur, the dimer must both be at one end of an excised fragment and contain an internal phosphodiester break. Taken together, these data lead us to propose a novel model for dimer repair in human cells in which hydrolysis of the intradimer phosphodiester linkage precedes the concerted action of a generalized ‘bulky lesion-repair complex’ involving conventional strand incision/lesion excision/repair resynthesis/strand ligation reactions.
Molecular Studies on the Nature of the Repair Defect in Ataxia-Telangiectasia and Their Implications for Cellular Radiobiology
Authors: Debenham P. G. , Webb M. B. T. , Jones N. J. , Cox R. 
Published: May 2013

ABSTRACT
We have utilized DNA transfer and recombinant DNA techniques to probe DNA double-strand break repair in the human ionizing radiation-sensitive genetic syndrome ataxia-telangiectasia (A-T). Using restriction enzyme-generated double-strand breaks in the coding sequence of a selectable gene we have detected a significantly greater frequency of mis-repair of such breaks in a permanent A-T cell line compared with cell lines of normal radiosensitivity. This mis-repair in A-T can plausibly explain many of the clinical features of the disease but was insufficiently detailed to address the broad problem of DNA repair mechanisms relevant to ionizing radiation-induced damage. To extend these observations of DNA double-strand break mis-repair we have now applied this type of repair assay to novel, de novo induced mammalian X-ray-sensitive cell lines and to appropriate Escherichia coli mutants. In both cellular systems we have now found some equivalence to the A-T repair defect. In particular, studies on one E. coli mutant have provided evidence suggesting an involvement of a topoisomerase activity in DNA double-strand break misrepair, which may be relevant to the biochemical defect in A-T.
DNA Synthesis in Irradiated Mammalian Cells
Authors: Painter Robert B. , Young Barbara R. 
Published: May 2013

ABSTRACT
One of the first responses observed in S phase mammalian cells that have suffered DNA damage is the inhibition of initiation of DNA replicons. In cells exposed to ionizing radiation, a singlestrand break appears to be the stimulus for this effect, whereby the initiation of many adjacent replicons (a replicon cluster) is blocked by a single-strand break in any one of them. In cells exposed to ultraviolet light (u.v.), replicon initiation is blocked at fluences that induce about one pyrimidine dimer per replicon. The inhibition of replicon initiation by u.v. in Chinese hamster cells that are incapable of excising pyrimidine dimers from their DNA is virtually the same as in cells that are proficient in dimer excision. Therefore, a single-strand break formed during excision repair of pyrimidine dimers is not the stimulus for inhibition of replicon initiation in u.v.-irradiated cells. Considering this fact, as well as the comparative insensitivity of human ataxia telangiectasia cells to u.v.-induced inhibition of replicon initiation, we propose that a relatively rare lesion is the stimulus for u.v.-induced inhibition of replicon initiation.
Molecular Signal for Induction of the Adaptive Response to Alkylation Damage in Esherichia Coli
Authors: Sedgwick B. 
Published: May 2013

ABSTRACT
Exposure of Escherichia coli to simple alkylating agents, such as methylnitrosourea, causes the induction of at least three DNA repair functions that are under the control of the ada gene. The ada gene product itself repairs several O-methylated lesions in DNA, including methylphosphotriesters and the mutagenic adduct O1-methylguanine. The methyl groups are transferred from these lesions on to two different cysteine residues within the Ada protein resulting in selfmethylation. We have found that the Ada protein is converted to an activator of expression of genes involved in the adaptive response after accepting a methyl group from a methylphosphotriester, but not from O1-methylguanine. This was shown using the in vitro techniques of DNA-dependent protein synthesis and run-off transcription. Delayed electrophoretic migration and footprinting experiments have shown that the methylated activator of transcription binds to specific DNA sequences immediately upstream from the RNA polymerase binding sites in the promoter regions of the inducible genes. The Ada protein-binding sites contain the common sequence d(A-A-A-N- N-A-A-A-G-C-G-C-A).
Nerve growth factors and molecules of the extracellular matrix in neuronal development
Authors: Edgar David 
Published: May 2013

ABSTRACT
The survival of developing neurons is epigenetically regulated by trophic factors. Only one such protein, the nerve growth factor (NGF) has been shown to act in vivo, where it supports the survival of neural-crest-derived sensory and sympathetic neurons. Recently, however, other proteins have been isolated and shown to support the survival of cultured neurons. Furthermore, in addition to the effects of soluble trophic factors, proteins of the extracellular matrix are also able to modulate neuronal survival. Analysis of the basal lamina protein, laminin, shows that when used as a culture substrate it stimulates neurite outgrowth and potentiates neuronal survival via a site associated with its heparin binding domain. On proteolytic cleavage of laminin, however, a cryptic site is unmasked that can also promote neuronal survival and neurite growth. The properties of this cryptic site indicate that it may be similar to that of the laminin-like molecule synthesized by Schwann cells, which although recognized by anti-laminin antibodies is not inhibited by them.
IN VIVO Aspects of urogastrone-epidermal growth factor
Authors: Gregory H. 
Published: May 2013

ABSTRACT
Recent evidence indicates that human urogastrone-epidermal growth factor originates in submandibular and Brunner’s glands and that serum levels are low (&lt;1ngml−1). It occurs in many secreted fluids to a much greater extent and many tissues are thus exposed to concentrations greater than 100 ng ml−1. Rapid actions in vivo of URO-EGF include the ability to inhibit gastric acid secretion at low doses (250 ng kgh−1 in humans) and to provide cytoprotective effects against ulcerogenic agents (250 ng kg h−1 in cats). More prolonged exposure of tissues shows increases in parameters related to wound healing, beneficial effects upon ulceration and also the ability to accelerate crypt cell production rate along the gastrointestinal tract. Synthetic material has been prepared with an identical structure to the natural URO-EGF thus enabling detailed studies of the biological effects to be pursued.
Activation and cell cycle control of murine b lymphocytes
Authors: Melchers Fritz , Corbel Catherine , Leptin Maria , Lernhardt Waldemar 
Published: May 2013

ABSTRACT
The cell cycle of activated murine B lymphocytes (B cells) is controlled by the occupancy of surface membrane-bound immunoglobulin (Ig) and by two types of growth factors, called α and β factors. These growth factors are produced in an endocrine fashion by the interaction of helper T lymphocytes (T cells) with antigen-presenting macrophages (A cells). Antigen is taken up, processed and presented on the surface of A cells in the context of class II major histocompatibility complex (MHC) glycoproteins. Helper Tcells recognize this association of antigen and class II MHC molecules. A cells produce "factors and T cells produce β factors. The molecular nature of these factors and of the corresponding receptors on B cells has yet to be elucidated, although it can be shown that the complement component C3d replaces αfactor action.
Resting, Go phase B cells are refractory to the action of α and β factors. They have to be excited, i.e. rendered susceptible to the action of these factors. This can be achieved by the interaction with helper T cells that recognize antigen, bound by surface membrane Ig, in the context of class II MHC glycoproteins on the surface of resting G0 B cells. Excitation can also occur in a polyclonal fashion by cross-linking of suface Ig with immobilized, Ig-specific antibodies, or by the interaction with polyclonal activators of B cells, such as lipopolysaccharides. Entry into the cell cycle is asynchronous. Activated, cycling B cells can be synchronized by size separation, using velocity sedimentation. Synchronized B cells will retain their synchrony for several divisions, when they are stimulated by immobilized Ig-specific antibodies, αand β factors. They divide every 20h at 37°C. Omission of either of the three stimuli arrests B cells, though at different points in the cell cycle. Three restriction points are found: the first occurs immediately after mitosis and is controlled by the binding of immobilized Ig-specific antibodies to surface membrane-bound Ig. The second is observed in the G1 phase, around 6-8 h after mitosis and 2-4h before entry into S phase. It is controlled by αfactors. The third is found 2-4 h before mitosis, in G2 phase, and is controlled by βfactors.
Polymer Sliding In Axons
Authors: J. Lasek Raymond 
Published: May 2013

ABSTRACT
In axons the cytoskeletal polymers are transported by slow axonal transport. Microtubules, microfilaments and neurofilaments move at different rates in the axon. On the basis of their transport rates, two populations of polymers can be distinguished: SCb polymers are transported at 2–4 mm day-1 and SCa polymers are transported at 0·25-l mmday~?. As they move within the axon’, the faster moving SCb polymers must pass the slower moving SCa polymers. This observation and others indicate that polymers slide in the axon. A model of polymer sliding is presented. This model provides a dynamic architectural framework for studies of the mechanisms of slow axonal transport.