bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the microbial community structure in Candidatus Liberibacter asiaticus-infected citrus plants treated with antibiotics in the field
Authors: Zhang Muqing , Powell Charles A , Guo Ying , Benyon Lesley , Duan Yongping 
Published: May 2013

AbstractBackgroundHuanglongbing (HLB) is a worldwide devastating disease of citrus. There are no effective control measures for this newly emerging but century-old disease. Previously, we reported a combination of Penicillin G and Streptomycin was effective in eliminating or suppressing the associated bacterium, ‘CandidatusLiberibacter asiaticus’ (Las).ResultsHere we report the bacterial composition and community structure in HLB-affected citrus plants during a growing season and while being treated with antibiotic combinations PS (Penicillin G and Streptomycin) and KO (Kasugamycin and Oxytetracycline) using the Phylochip™ G3 array. Both antibiotic treatments resulted in significantly lower Las bacterial titers (Pr<0.05) and hybridization scores. Of the 50,000+ available operational taxonomic units (OTUs) on PhyloChip™ G3, 7,028 known OTUs were present in citrus leaf midribs. These OTUs were from 58 phyla, of which five contained 100 or more OTUs,Proteobacteria(44.1%), Firmicutes(23.5%),Actinobacteria(12.4%),Bacteroidetes(6.6%) andCyanobacteria(3.2%). In the antibiotic treated samples, the number of OTUs decreased to a total of 5,599. The over-all bacterial diversity decreased with the antibiotic treatments, as did the abundance of 11 OTUs withinProteobacteria,Firmicutes,BacteroidetesandPlanctomycetes. Within theProteobacteria, ten OTUs representing the classγ-proteobacteria increased in abundance after four months of treatment, when the Las bacterium was at its lowest level in the HLB-affected citrus field plants.ConclusionsOur data revealed thatProteobacteriawas constantly the dominant bacterial phylum recovered from citrus leaf midribs, with the α-proteobacterial and the γ-proteobacterial classes vying for prevalence. In addition, the level of bacterial diversity found in the leaf midribs of field citrus was greater than previously described. Bacterial cells in close proximity may be able to modify their microenvironment, making the composition of the microbial community an important factor in the ability of Las to cause HLB progression. A low Las level was seen as an annual fluctuation, part of the bacterial population dynamics, and as a response to the antibiotic treatments.
Intracardiac metastasis from known cervical cancer: a case report and literature review
Authors: Byun Seung Won , Park Sung Taek , Ki Eun Young , Song Hyun , Hong Suk Hee , Park Jong Sup 
Published: May 2013

Abstract
Cardiac metastasis from known cervical cancer is rare. Even through a routine check-up, this type of metastasis can present as pulmonary emboli. Suspicion of this diagnosis in an oncology patient with complicating pulmonary emboli but no evidence of deep vein thrombosis is important, especially in cervical cancer patients with extensive pelvic lymph node metastasis and vascular invasion of a primary tumor. Early recognition may aid in improving the prognosis. We present a case of intracardiac metastasis arising from a squamous carcinoma of the cervix in a patient with pulmonary tumor emboli and review other cases from the literature.
Monoubiquitination of EEA1 regulates endosome fusion and trafficking
Authors: Ramanathan Harish N , Zhang Guofeng , Ye Yihong 
Published: May 2013

Abstract

Background
Early endosomal autoantigen 1 (EEA1) is a membrane tethering factor required for the fusion and maturation of early endosomes in endocytosis. How the activity of EEA1 is regulated in cells is unclear.

Results
Here we show that endogenous EEA1 is prone to monoubiquitination at multiple sites, owing to an intrinsic affinity to ubiquitin conjugating enzymes (E2). The E2 interactions enable a ubiquitin ligase (E3) independent mechanism that decorate EEA1 with multiple mono-ubiquitin moieties. Expression of an ubiquitin-EEA1 chimera that mimics native mono-ubiquitinated EEA1 generates giant endosomes abutting the nucleus. Several lines of evidence suggest that this phenotype is due to increased endosome fusion and a simultaneous blockade on an endosome recycling pathway. The latter is likely caused by diminished endosome fission in cells expressing ubiquitin-EEA1.

Conclusion
Our results demonstrate that ubiquitination may dramatically affect the activity of an endosome fusion factor to alter endosome morphology and trafficking pattern, and thereby implicating an unexpected role of ubiquitin signaling in endocytosis.
Genetic Evidence for Nucleotide Excision Repair of O6-Alkylguanine in Mammalian Cells
Authors: Boyle J. M. , Durrant L. G. , Wild C. P. , Saffhill R. , Margison G. P. 
Published: May 2013

ABSTRACT
Human cells that lack O1-alkylguanine DNA alkyltransferase (AT) activity can remove O1-butylguanine (O1-wBuG) produced in cellular DNA by exposure to N-n-butyl-N-nitrosourea as determined by radioimmunoassay of enzyme digests of DNA. Fibroblasts from xeroderma pigmentosum (XP) complementation groups A and G that show &lt;5 % unscheduled DNA synthesis following exposure to UVC failed to remove O1-nBuG. Hence it appears that O1- alkylguanine is repaired in cells that lack AT by a process that is defective in XP cells, presumably nucleotide excision repair. Neither V79 nor V79/79 Chinese hamster cell lines have AT activity and both are able to remove O1-nBuG from DNA. However, only V79/79 is able to remove O1MeG, suggesting some substrate specificity of the excision repair process. Comparison of relative levels of O1-alkylation by N-mcthyl-, N-ethyl-, N-propyl- and N-n-butyl-nitrosourea indicate that approximately equal levels of O1-alkylation are produced by equitoxic doses of these agents.
DNA Repair in Specific Sequences in Mammalian Cells
Authors: Smith Charles A. 
Published: May 2013

ABSTRACT
To investigate the influence of function or activity of a DNA sequence on its repair, we have studied excision repair of a number of adducts in the non-transcribed, heterochromatic alpha DNA of monkey cells (by physically isolating the DNA) and also the removal of pyrimidine dimers in a number of genes in rodent and human cells (by an indirect assay using a dimer-specific endonuclease). In confluent cells, psoralen and aflatoxin B] (AFB1) adducts are produced in similar frequencies in alpha and in the rest of the DNA, but removal from alpha is severely deficient. Adducts of A’-acetoxy acetyl aminofluorene (NA-AAF) are formed in slightly higher frequencies in alpha, and removal is slightly deficient. The removal of thymine glycols from alpha DNA in gamma-irradiated cells is proficient, as is repair synthesis elicited by exposure to methyl methane sulphonate, dimethyl sulphate, or 254nm ultraviolet light (u.v.). Removal of AFB1 and NA-AAF adducts from alpha is enhanced by small doses of u.v. but not by X-rays or DMS. The quantum efficiency of conversion of psoralen monoadducts to crosslinks is much lower in alpha DNA. Taken together, these results suggest that the highly condensed chromatin structure of alpha hinders access of the repair system that acts on bulky adducts but not of systems for repair of specific base damage, u.v. damage may alter this chromatin structure directly or facilitate the action of some system that changes accessibility of chromatin to repair. The repair deficiencies are not observed in actively growing cells, in which chromatin structure may be less condensed due to DNA replication.
We have also demonstrated preferential excision repair of pyrimidine dimers in active genes. Dimers are efficiently removed from the essential dihydrofolate reductase (DHFR) and hydroxy- methylglutaryl CoA reductase genes in Chinese hamster ovary (CHO) cells and from the transcribed c-ahl proto-oncogene in the mouse cells. Both cell types remove few dimers from their overall genomes or from sequences distal to the DHFR gene; dimers are also removed poorly from the non-transcribed mouse c-mos gene. In human cells, dimers are removed more rapidly from the DHFR gene than from the genome as a whole. However, repair is as deficient in this gene in XP-C cells as it is in the entire genome.
These results suggest that resistance to DNA damage correlates better with repair of vital or active sequences than with overall repair levels and that mutagenic efficiency may vary according to the activity of the gene under study.
DNA Repair Mutants in Higher Eukaryotes
Authors: Collins A. , Johnson R. T. 
Published: May 2013

ABSTRACT
Over the past ten years or so, we have seen a proliferation of reports of new cell lines of various vertebrate species, showing hypersensitivity to killing by DNA damaging agents. Regrettably, but predictably, there is no standard terminology to describe the mutants, and as a result the literature is liberally scattered with fragments of individualistic nomenclature. There is no way of imposing order at this stage, but it may be helpful to bring together in this chapter as much information as possible on the mutants now available. As well as being an aid for reference, this should serve as a pointer towards further investigation - either in characterizing the mutants we have, or in developing new ones to fill gaps in our knowledge.
Functional Expression of the Escherichia Coli Alkyltransferase Gene in Mammalian Cells
Authors: Margison G. P. , Brennand J. 
Published: May 2013

ABSTRACT
Alkylating agents can produce a variety of biological effects in mammalian cells and organisms including toxicity, mutagenicity and malignant transformation. These agents react with oxygen and nitrogen atoms in DNA resulting in 12 products some of which are known to be eliminated from DNA by repair systems. One method of assessing the relative importance of a specific product in any of the biological effects of DNA alkylation would be to convert a cell line that is deficient in a particular repair function into a repair-proficient cell line and to determine whether this influences the magnitude of the effect. The cloning and expression in mammalian cells of the Escherichia coli DNA repair gene coding for the O1-alkylguanine-alkylphosphotriester dual alkyltransferase will be described. The E. coli gene product acts on damage produced in host cell DNA by treatment with methylnitrosourea, and reduces the toxicity and mutagenicity of this agent. The effects on the toxicity of a variety of other mono and bifunctional alkylating agents have also been assessed.
Recent Progress with the DNA Repair Mutants of Chinese Hamster Ovary Cells
Authors: Thompson L. H. , Salazar E. P. , Brookman K. W. , Collins C. C. , Stewart S. A. , Busch D. B. , Weber C. A. 
Published: May 2013

ABSTRACT
Repair-deficient mutants of Chinese hamster ovary (CHO) cells are being used to identify human genes that correct the repair defects and to study mechanisms of DNA repair and mutagenesis. Five independent tertiary DNA transformants were obtained from the EM9 mutant, which is noted for its very high sister-chromatid exchange frequencies. In these clones a human DNA sequence was identified that correlated with the resistance of the cells to chlorodeoxyuridine (CldUrd). After Eco RI digestion, Southern transfer, and hybridization of transformant DNAs with the BLUR-8 Alu family sequence, a common fragment of 25-30 kilobases (kb) was present. Since the DNA molecules used to produce these transformants were sheared to &lt;50 kb in size, the correcting gene should be small enough to clone in a cosmid vector.
Using drug-resistance markers to select for hybrids after fusion, we have done complementation experiments with ultraviolet light (u.v.)-sensitive mutants and have identified a sixth complementation group, line UV61. Additionally, CHO mutants UV27-1 and MMC-2, isolated in other laboratories, were found to belong to UV group 3, which is represented by line UV24.
To study the behaviour of transfected DNA molecules in repair-deficient cells, we treated plasmid pSN2gpt with either u.v. radiation or cA-diamminedichloroplatinum(II) (cA-DDP) and introduced the damaged DNA into normal CHO cells (AA8) and mutants UV4 and UV5. Unrepaired damage to the plasmid was indicated by loss of colony-forming ability of the transfected cells in selective medium containing mycophenolic acid. With u.v. damage, the differential survival of the cell lines was similar to that seen when whole cells are treated with u.v. However, with cw-DDP damage, mutant UV4 did not exhibit the extreme hypersensitivity (50-fold) that occurs when cells are treated. This result suggests that UV4 cells may be able to repair cross-links in transfected DNA.
Surface components involved in bacterial pathogen-plant host recognition
Authors: Sequeira Luis 
Published: May 2013

ABSTRACT
During their initial association with plant hosts, pathogenic bacteria interact with plant cell walls. The results of this interaction appear to determine whether bacterial multiplication will take place. With one group of bacterial plant pathogens (e.g. Agrobacterium tumefaciens), attachment to the host surface appears essential for pathogenesis. With another group (e.g. Pseudomonas solanacearum), only those strains that do not attach to the host cell wall are able to multiply in the intercellular spaces. Attachment of many incompatible strains to tobacco mesophyll cell walls leads to a rapid hypersensitive response (HR) and a drastic reduction in bacterial multiplication. Our working hypothesis is that these differences in host response to strains of P. solanacearum are the result of a recognition response in which surface components of both host and pathogen play important roles.
Our approach is based on the use of spontaneous or transposon (Tn5)-generated mutants of strains K60 (virulent) and Bl (avirulent) that differ in surface components and in their ability to attach to host cells and to induce the HR. A study of the surface components of bacterial and tobacco cell walls has led to the tentative conclusion that bacterial lipopolysaccharide (LPS) and plant hydroxyproline-rich glycoproteins mediate initial attachment, apparently as a result of charge-charge interaction. This initial attachment is reversed by high salt concentrations during the first 15 min, but not thereafter. Firm attachment appears to depend on hydrophobic interactions mediated by bacterial pili. At the normal ionic strength of intercellular fluids, extracellular polysaccharide (EPS) appears to inhibit only the pili-mediated attachment. Several HR− mutants of strain Bl have been obtained by Tn5 insertion, but they remain avirulent on tobacco. We are examining the EPS, LPS and pili production, and the attachment characteristics of these strains.
Rhizobium attachment to clover roots
Authors: Mills Kim K. , Bauer Wolfgang D. 
Published: May 2013

ABSTRACT
The adhesion of rhizobia to surfaces of clover roots was examined by an indirect plate-counting assay and phase-contrast microscopy. The number oí Rhizobium trifolii cells attached to clover root segments increased in approximately linear fashion during the first hour of incubation, but did not change appreciably thereafter. The addition of 30 mM-2-deoxy-D-glucose, which effectively inhibits binding of clover root lectin, did not promote the release of previously attached bacteria nor inhibit subsequent attachment to either root segments or root hairs. Rhizobia of several heterologous species attached to clover roots in numbers comparable to those of strains of R. trifolii, the homologous species. These results indicate that rhizobia have effective mechanisms of adhesion to non-host roots and that clover lectin contributed little or nothing to attachment under the conditions examined.
Cell wall glycoproteins: structure and function
Authors: Roberts K. , Grief C. , Hills G. J. , Shaw P. J. 
Published: May 2013

ABSTRACT
Hydroxyproline-rich glycoproteins form an important, but little understood, structural component of most cell walls. Their occurrence, chemistry, synthesis, secretion, cross-linking and functions in higher plant cell walls will be briefly reviewed. Similar molecules also occur in other groups of plants; in particular, in the algae. In many of these they form highly ordered cell surface arrays, and we have studied these by high-resolution electron microscopy and computer image reconstruction. Some resulting three-dimensional models of these are presented. One particular glycoprotein, the major structural component of the cell wall of Chlamydonwnas reinhardii, has been investigated in some detail. The chemistry and structure of this glycoprotein, which we have called volvin, has. been studied and a family of monoclonal antibodies has been raised against it. Some of these antibodies appear to be specific to oligosaccharide side-chains and allow the localization of these substituents and their sites of synthesis. Immunofluorescence studies have shown that the expression of some of these antigenic determinants is developmentally regulated or cell-cycle-dependent. Immunogold labelling of thin sections has enabled the sites of synthesis and the method of secretion to be determined. These results will be discussed in the context of other cell wall glycoproteins, their relation to other glycoproteins, such as the mating agglutinin, and to their possible functions.
Differences and similarities in the neurotrophic growth factor requirements of sensory neurons derived from neural crest and neural placode
Authors: Lindsay Ronald M. , Barde Yves-Alain , Davies Alun M. , Rohrer Hermann 
Published: May 2013

ABSTRACT
This article reviews recent studies that have examined differences and similarities in the neurotrophic growth factor requirements of neural crest-and neural placode-derived sensory neurons of the developing chick embryo. From in vitro experiments using both explant and dissociated, neuron-enriched cultures of spinal and cranial nerve sensory neurons, it has been established that only sensory neurons of neural crest origin are responsive, at least in terms of survival and neurite outgrowth, to mouse submandibular gland nerve growth factor (NGF). Sensory neurons derived from neural placodes (neurons of the ventrolateral portion of the trigeminal ganglion and the entire neuronal population of the vestibular, geniculate, petrosal and nodose ganglia) are largely unresponsive to NGF throughout embryonic development, but do respond to neurotrophic activity present in extracts of brain and various peripheral ‘end-organs’, such as heart or liver. By incubation of neuron-enriched cultures with radiolabelled [125I]NGF, followed by autoradiographic exposure, it has been demonstrated that placode-derived neurons, in marked contrast to those of neural crest origin, are completely devoid of specific cell surface receptors for NGF. In contrast to differences in their requirement and responsiveness to NGF, both placode-and crest-derived sensory neurons are responsive to the survival and neurite-promoting activity of a recently purified brain-derived neurotrophic factor (BDNF). It is postulated that all primary sensory neurons have a dual growth factor requirement during development; their survival being dependent on a supply of both a peripheral and a central ‘target’-derived neurotrophic factor. It appears that BDNF may act as common ‘central target-derived’ neurotrophic factor for both placode-and crest-derived sensory neurons, but that within peripheral tissues there are specific neurotrophic factors for each of these two classes of primary sensory neurons.
Analysis Of Pseudopodial Structure And Assembly With Viral Projections
Authors: A. Mortara Renato , L. E. Koch Gordon 
Published: May 2013

ABSTRACT
The mechanisms by which cells extend motile pseudopodial projections are still poorly understood. Several fundamental mechanisms have been proposed on the basis of hydrostatic pressure, membrane addition and microfilament reorganization. A common focus of all such mechanisms is the growing tip of a pseudopodium. Yet some basic questions about the nature of the tip in natural pseudopodia remain obscure. However, one class of structure, the virus-tipped projections, often contains a well-defined particle, both morphologically and biochemically, and therefore provides a useful model system for the examination of the tips of cellular projections.
In P815 cells the virus-tipped projections are long, thin structures closely resembling filopodia in other cells. The apical virus particle is a retrovirus particle produced by the chronic infection existing in this cell line. In demembranated filopodia, the virus particle retains a tight association with a single actin microfilament. Biochemical analyses indicate that the major retroviral structural polypeptide Pr65 is an actin-binding protein that could provide the anchorage site for the actin filament.
The existence of a solid virus particle tethered by an actin filament to the cytoskeleton makes it very unlikely that these projections grow by membrane addition at the tip. The major positive implication is that the apex of a projection does not relinquish’ its interaction with the submembranous cytoskeleton during growth. Such an arrangement would be compatible with either a hydrostatic-pressure-driven or a cytoskeleton-driven mechanism of filopodial growth.
Dna transposition between plant organellar genomes
Authors: Stern David B. 
Published: May 2013

ABSTRACT
Higher plant mitochondrial and chloroplast DNAs are known to share extensive sequence homologies. The present work addresses issues raised by these initial observations: (1) what is the distributive pattern of ctDNA sequences among different mitochondrial genomes, (2) what is the frequency of DNA transposition between the two organelles, (3) are the transposed ctDNA sequences transcribed? The results to be presented demonstrate that many ctDNA sequences, including identified genes, are widespread in mitochondrial genomes and in some cases are highly conserved. However, the distribution of any one particular sequence is sporadic, even within a plant family. Preliminary data, obtained in studies of watermelon, raise the possibility that some mtDNA transcripts share homology with ctDNA sequences.