Variation of extrachromosomal circular DNA in cancer cell lines.

The presence of oncogene carrying eccDNAs is strongly associated with carcinogenesis and poor patient survival. Tumour biopsies and in vitro cancer cell lines are frequently utilized as models to investigate the role of eccDNA in cancer. However, eccDNAs are often lost during the in vitro growth of cancer cell lines, questioning the reproducibility of studies utilizing cancer cell line models. Here, we conducted a comprehensive analysis of eccDNA variability in seven cancer cell lines (MCA3D, PDV, HaCa4, CarC, MIA-PaCa-2, AsPC-1, and PC-3). We compared the content of unique eccDNAs between triplicates of each cell line and found that the number of unique eccDNA is specific to each cell line, while the eccDNA sequence content varied greatly among triplicates (∼ 0-1% eccDNA coordinate commonality). In the PC-3 cell line, we found that the large eccDNA (ecDNA) with MYC is present in high-copy number in an NCI cell line isolate but not present in ATCC isolates. Together, these results reveal that the sequence content of eccDNA is highly variable in cancer cell lines. This highlights the importance of testing cancer cell lines before use, and to enrich for subclones in cell lines with the desired eccDNA to get relatively pure population for studying the role of eccDNA in cancer.

Plant adaptation to low phosphorus availability: Core signaling, crosstalks, and applied implications.

Phosphorus (P) is an essential nutrient for plant growth and reproduction. Plants preferentially absorb P as orthophosphate (Pi), an ion that displays low solubility and that is readily fixed in the soil, making P limitation a condition common to many soils and Pi fertilization an inefficient practice. To cope with Pi limitation, plants have evolved a series of developmental and physiological responses, collectively known as the Pi starvation rescue system (PSR), aimed to improve Pi acquisition and use efficiency (PUE) and protect from Pi-starvation-induced stress. Intensive research has been carried out during the last 20 years to unravel the mechanisms underlying the control of the PSR in plants. Here we review the results of this research effort that have led to the identification and characterization of several core Pi starvation signaling components, including sensors, transcription factors, microRNAs (miRNAs) and miRNA inhibitors, kinases, phosphatases, and components of the proteostasis machinery. We also refer to recent results revealing the existence of intricate signaling interplays between Pi and other nutrients and antagonists, N, Fe, Zn, and As, that have changed the initial single-nutrient-centric view to a more integrated view of nutrient homeostasis. Finally, we discuss advances toward improving PUE and future research priorities.

Biological traits of the predatory mirid Macrolophus praeclarus, a candidate biocontrol agent for the Neotropical region.

The predatory mirid Macrolophus praeclarus is widely distributed throughout the Americas, and is reported to prey upon several horticultural pest species. However, little is known about its biology, thermal requirements, crop odour preferences, phytophagy, and capability to induce defensive responses in plants. When five temperatures studied (20, 25, 30, 33 and 35°C) were tested and Ephestia kuehniella was used as prey, the developmental time from egg to adult on tomato, was longest at 20°C (56.3 d) and shortest at 33°C (22.7 d). The ability of nymphs to develop to adults decreased as the temperature increased, with the highest number of nymphs reaching the adult stage at 20°C (78.0%) and lowest at 35°C (0%). The lower and upper developmental thresholds were estimated at 11.2° and 35.3°C, respectively. The maximum developmental rate occurred at 31.7°C and the thermal constant was 454.0 ± 8.1 degree days. The highest predation rate of E. kuehniella eggs was obtained at 30°C. In Y-tube olfactory choice tests, M. praeclarus selected tomato, sweet pepper and eggplant odours more frequently than no plant control treatment. Macrolophus praeclarus feeding did not damage tomato plants compared to another zoophytophagous mirid, Nesidiocoris tenuis, which caused necrotic rings. The phytophagy of M. praeclarus induced defensive responses in tomato plants through the upregulation of the jasmonic acid metabolic pathway. The implications of the findings for using M. praeclarus in tomato biological control programmes in the Americas are discussed.

Novel signals in the regulation of Pi starvation responses in plants: facts and promises.

Plants have evolved numerous adaptive developmental and metabolic responses to cope with growth in conditions of limited phosphate (Pi). Regulation of these Pi starvation responses (PSR) at the organism level involves not only cellular Pi perception in different organs, but also inter-organ communication of Pi levels via systemic signaling. Here we summarize recent discoveries on Pi starvation sensing and signaling, with special emphasis on structure-function studies that showed a role for inositol polyphosphates (InsP) as intracellular Pi signals, and on genomic studies that identified a large number of mRNAs with inter-organ mobility, which provide an immense source of potential systemic signals in the control of PSR and other responses.

Dot Blot para determinar la identidad antigénica en vacunas conjugadas contra Streptococcus pneumoniae serotipo 19F / Dot Blot to determine the antigenic identity in conjugated vaccines against Streptococcus pneumoniae serotype 19F

Las autoridades regulatorias recomiendan el uso de técnicas de Resonancia Magnética Nuclear o técnicas serológicas para la determinación de la identidad de los antígenos presentes en las vacunas conjugadas. Con la aparición de las vacunas conjugadas multivalentes, se ha hecho necesario recurrir a técnicas inmunoquímicas con la utilización de anticuerpos monoclonales para aumentar la sensibilidad en la determinación de la identidad de los antígenos en dichas vacunas conjugadas. El objetivo del presente trabajo fue establecer las condiciones óptimas de trabajo que permitieran utilizar la técnica del Dot Blot para determinar la identidad de los antígenos en vacunas conjugadas de Streptococcus pneumoniae serotipo 19F. Para ello se estudiaron los tiempos de incubación, la influencia del reactivo en la solución de bloqueo; también las concentraciones óptimas del anticuerpo monoclonal y de los ingredientes farmacéuticos activos, así como los volúmenes de aplicación óptimos para estos y vacunas. Se utilizó un anticuerpo monoclonal contra el polisacárido capsular del serotipo 19F de neumococo. Las muestras empleadas en este trabajo fueron lotes de ingredientes farmacéuticos activos de conjugados de polisacárido capsular 19F y lotes de un candidato vacunal cubano conjugado heptavalente contra neumococos. Los resultados mostraron que para la determinación de la identidad antigénica fueron suficientes 10 µL de muestras de los principios activos a una concentración de 125 µg/mL e igual volumen para las vacunas heptavalentes. Quedó demostrado que una concentración de 1 µg/mL para el anticuerpo monoclonal y tiempos de incubación de 30 min a 37 °C fueron suficientes para la determinación. Estos resultados permiten concluir que quedaron establecidas las condiciones óptimas de trabajo para determinar la identidad antigénica por Dot Blot del polisacárido capsular de S. pneumoniae serotipo 19F presente en las vacunas conjugadas(AU)

Regulatory authorities recommend the use of NMR (Nuclear Magnetic Resonance) techniques or serological techniques to determine the identity of antigens on the conjugate vaccines. Due to the emergence of multivalent conjugate vaccines it has become necessary to use immunochemical techniques with the use of monoclonal antibodies (MAbs) in order to increase the sensitivity in determining the identity of such antigen in the conjugate vaccines. The aim of this study was to establish the optimal working conditions that would allow using Dot Blot technique to determine the identity of antigens in conjugate vaccines against Streptococcus pneumoniae serotype 19F. The incubation times, the possibility of using different reagents for blocking step were studied for this purpose; also the optimal concentrations of MAbs and active pharmaceutical ingredients (APIs), as well as the volumes of optimal application for APIs and vaccines. A monoclonal antibody against the capsular polysaccharide of S. pneumoniae serotype 19F (PsC 19F) was used. The samples used in this work, were samples of lots of APIs of monovalent conjugated PsC 19F and lots of Cuban heptavalent conjugate vaccine candidate against pneumococcus. The results showed that for the determination of the antigenic identity were optimal volumes of 10 µL of monovalent conjugate samples at 125 µg/mL and equal volume for heptavalent vaccines. For MAb was demonstrated that 1 µg/mL concentration of MAb against the PSC 19F and incubation times of 30 min at 37 °C were sufficient to successfully perform the determinations. In conclusion we can say that were established optimal working conditions to determine the antigenic identity, by Dot Blot, for the capsular polysaccharide of S. pneumoniae serotype 19F present in the APIs of monovalent conjugated and in the heptavalent conjugate vaccines(AU)

Dot Blot para determinar la identidad antigénica en vacunas conjugadas contra Streptococcus pneumoniae serotipo 19F / Dot Blot to determine the antigenic identity in conjugated vaccines against Streptococcus pneumoniae serotype 19F

Las autoridades regulatorias recomiendan el uso de técnicas de Resonancia Magnética Nuclear o técnicas serológicas para la determinación de la identidad de los antígenos presentes en las vacunas conjugadas. Con la aparición de las vacunas conjugadas multivalentes, se ha hecho necesario recurrir a técnicas inmunoquímicas con la utilización de anticuerpos monoclonales para aumentar la sensibilidad en la determinación de la identidad de los antígenos en dichas vacunas conjugadas. El objetivo del presente trabajo fue establecer las condiciones óptimas de trabajo que permitieran utilizar la técnica del Dot Blot para determinar la identidad de los antígenos en vacunas conjugadas de Streptococcus pneumoniae serotipo 19F. Para ello se estudiaron los tiempos de incubación, la influencia del reactivo en la solución de bloqueo; también las concentraciones óptimas del anticuerpo monoclonal y de los ingredientes farmacéuticos activos, así como los volúmenes de aplicación óptimos para estos y vacunas. Se utilizó un anticuerpo monoclonal contra el polisacárido capsular del serotipo 19F de neumococo. Las muestras empleadas en este trabajo fueron lotes de ingredientes farmacéuticos activos de conjugados de polisacárido capsular 19F y lotes de un candidato vacunal cubano conjugado heptavalente contra neumococos. Los resultados mostraron que para la determinación de la identidad antigénica fueron suficientes 10 µL de muestras de los principios activos a una concentración de 125 µg/mL e igual volumen para las vacunas heptavalentes. Quedó demostrado que una concentración de 1 µg/mL para el anticuerpo monoclonal y tiempos de incubación de 30 min a 37 °C fueron suficientes para la determinación. Estos resultados permiten concluir que quedaron establecidas las condiciones óptimas de trabajo para determinar la identidad antigénica por Dot Blot del polisacárido capsular de S. pneumoniae serotipo 19F presente en las vacunas conjugadas(AU)

Regulatory authorities recommend the use of NMR (Nuclear Magnetic Resonance) techniques or serological techniques to determine the identity of antigens on the conjugate vaccines. Due to the emergence of multivalent conjugate vaccines it has become necessary to use immunochemical techniques with the use of monoclonal antibodies (MAbs) in order to increase the sensitivity in determining the identity of such antigen in the conjugate vaccines. The aim of this study was to establish the optimal working conditions that would allow using Dot Blot technique to determine the identity of antigens in conjugate vaccines against Streptococcus pneumoniae serotype 19F. The incubation times, the possibility of using different reagents for blocking step were studied for this purpose; also the optimal concentrations of MAbs and active pharmaceutical ingredients (APIs), as well as the volumes of optimal application for APIs and vaccines. A monoclonal antibody against the capsular polysaccharide of S. pneumoniae serotype 19F (PsC 19F) was used. The samples used in this work, were samples of lots of APIs of monovalent conjugated PsC 19F and lots of Cuban heptavalent conjugate vaccine candidate against pneumococcus. The results showed that for the determination of the antigenic identity were optimal volumes of 10 µL of monovalent conjugate samples at 125 µg/mL and equal volume for heptavalent vaccines. For MAb was demonstrated that 1 µg/mL concentration of MAb against the PSC 19F and incubation times of 30 min at 37 °C were sufficient to successfully perform the determinations. In conclusion we can say that were established optimal working conditions to determine the antigenic identity, by Dot Blot, for the capsular polysaccharide of S. pneumoniae serotype 19F present in the APIs of monovalent conjugated and in the heptavalent conjugate vaccines(AU)

Endogenous Arabidopsis messenger RNAs transported to distant tissues.

The concept that proteins and small RNAs can move to and function in distant body parts is well established. However, non-cell-autonomy of small RNA molecules raises the question: To what extent are protein-coding messenger RNAs (mRNAs) exchanged between tissues in plants? Here we report the comprehensive identification of 2,006 genes producing mobile RNAs in Arabidopsis thaliana. The analysis of variant ecotype transcripts that were present in heterografted plants allowed the identification of mRNAs moving between various organs under normal or nutrient-limiting conditions. Most of these mobile transcripts seem to follow the phloem-dependent allocation pathway transporting sugars from photosynthetic tissues to roots via the vasculature. Notably, a high number of transcripts also move in the opposite, root-to-shoot direction and are transported to specific tissues including flowers. Proteomic data on grafted plants indicate the presence of proteins from mobile RNAs, allowing the possibility that they may be translated at their destination site. The mobility of a high number of mRNAs suggests that a postulated tissue-specific gene expression profile might not be predictive for the actual plant body part in which a transcript exerts its function.

Major QTLs control resistance to rice hoja blanca virus and its vector Tagosodes orizicolus.

Rice hoja blanca (white leaf) disease can cause severe yield losses in rice in the Americas. The disease is caused by the rice hoja blanca virus (RHBV), which is transmitted by the planthopper vector Tagosodes orizicolus. Because classical breeding schemes for this disease rely on expensive, time-consuming screenings, there is a need for alternatives such as marker-aided selection. The varieties Fedearroz 2000 and Fedearroz 50, which are resistant to RHBV and to the feeding damage caused by T. orizicolus, were crossed with the susceptible line WC366 to produce segregating F2:3 populations. The F3 families were scored for their resistance level to RHBV and T. orizicolus. The F2:3 lines of both crosses were genotyped using microsatellite markers. One major QTL on the short arm of chromosome 4 was identified for resistance to RHBV in the two populations. Two major QTL on chromosomes 5 and 7 were identified for resistance to T. orizicolus in the Fd2000 × WC366 and Fd50 × WC366 crosses, respectively. This comparative study using two distinct rice populations allowed for a better understanding of how the resistance to RHBV and its vector are controlled genetically. Simple marker-aided breeding schemes based on QTL information can be designed to improve rice germplasm to reduce losses caused by this important disease.

Proteomics identifies ubiquitin-proteasome targets and new roles for chromatin-remodeling in the Arabidopsis response to phosphate starvation.

In order to identify new regulators of the phosphate (Pi) starvation signaling pathway in plants, we analyzed variation in the abundance of nuclear-enriched proteins isolated from Arabidopsis roots that depends on Pi supply. We used 2-D fluorescence difference gel electrophoresis and MALDI-TOF/TOF techniques for proteome separation, visualization and relative protein abundance quantification and identification. Pi-controlled proteins identified in our analysis included components of the chromatin remodeling, DNA replication, and mRNA splicing machineries. In addition, by combining Pi starvation conditions with proteasome inhibitor treatments, we characterized the role of the ubiquitin-proteasome system, a major mechanism for targeted protein degradation in eukaryotes, in the control of the stability of Pi-responsive proteins. Among Pi-responsive proteins, the histone chaperone NAP1;2 was selected for further characterization, and was shown to display differential nucleo-cytoplasmic accumulation in response to Pi deprivation. We also found that mutants affecting three members of the NAP1 family accumulate lower Pi levels and display reduced expression of Pi starvation-inducible genes, reflecting a potential regulatory role for these chromatin-remodeling proteins in Pi homeostasis. BIOLOGICAL SIGNIFICANCE: In this study, we explore the feasibility of nuclear proteomics to identify regulatory proteins and ubiquitin-proteasome targets within a specific stress signaling pathway in plants, in our case phosphate starvation signaling in Arabidopsis. It will be of interest for researchers involved in the dissection of any signaling pathway in plants, in particular those with an interest in the ubiquitin-proteasome functions, and for the plant nutrition community.

Roles of ubiquitination in the control of phosphate starvation responses in plants(f).

Throughout evolution, plants have evolved sophisticated adaptive responses that allow them to grow with a limited supply of phosphate, the preferential form in which the essential macronutrient phosphorus is absorbed by plants. Most of these responses are aimed to increase phosphate availability and acquisition through the roots, to optimize its usage in metabolic processes, and to protect plants from the deleterious effects of phosphate deficiency stress. Regulation of these adaptive responses requires fine perception of the external and internal phosphate levels, and a complex signal transduction pathway that integrates information on the phosphate status at the whole-plant scale. The molecular mechanisms that participate in phosphate homeostasis include transcriptional control of gene expression, RNA silencing mediated by microRNAs, regulatory non-coding RNAs of miRNA activity, phosphate transporter trafficking, and post-translational modification of proteins, such as phosphorylation, sumoylation and ubiquitination. Such a varied regulatory repertoire reflects the complexity intrinsic to phosphate surveying and signaling pathways. Here, we describe these regulatory mechanisms, emphasizing the increasing importance of ubiquitination in the control of phosphate starvation responses.

Plant hormones and nutrient signaling.

Plants count on a wide variety of metabolic, physiological, and developmental responses to adapt their growth to variations in mineral nutrient availability. To react to such variations plants have evolved complex sensing and signaling mechanisms that allow them to monitor the external and internal concentration of each of these nutrients, both in absolute terms and also relatively to the status of other nutrients. Recent evidence has shown that hormones participate in the control of these regulatory networks. Conversely, mineral nutrient conditions influence hormone biosynthesis, further supporting close interrelation between hormonal stimuli and nutritional homeostasis. In this review, we summarize these evidences and analyze possible transcriptional correlations between hormonal and nutritional responses, as a means to further characterize the role of hormones in the response of plants to limiting nutrients in soil.