Suspended Particulate Matter in the Río de la Plata: importance in its spatial and temporal variability of the Bermejo river

[EN] Spatio-temporal variability of Suspended Particulate Matter (SPM) in the Río de la Plata (RdlP) is analyzed from 2002-2014 of MODIS (Moderate Resolution Imaging Spectroradiometer) data and explained in terms of its main tributaries flows. The monthly mean showed maximum during late summer to mid-autumn, and minimum in mid-winter to early summer. The Bermejo river (BeR), is the tributary that more sediment in suspension brings. This situation was reflected in the significant relationship between the mean monthly concentrations of SPM with the average monthly flow of BeR. Seasonal variation in SPM concentration, showed maximum values in fall, followed by summer, and minimum values in winter and spring, reflecting the monthly pattern of discharge of the BeR with one and two months of delay. The pattern of spatial variation differentiated threes regions: the inner, central and outer. The annual variability evidenced a marked seasonality in the spatial coverage pattern of the waters with the highest SPM. The pattern of the anomalies, appeared to be related to the influence of river discharge, what it showed the temporal pattern of SPM anomalies did not related to the ENSO (El Niño – Sourthen Oscillation) cycle. These results allowed us to denote the importance of BeR (not ENSO dependent) to explain the pattern of observed SPM anomaly in the RdlP region.[ES] La variabilidad espacio-temporal del Material Particulado en Suspensión (MPS) en el Río de la Plata (RdlP) fue analizada para el periodo 2002-2014 a partir de datos Aqua-MODIS (Moderate Resolution Imaging Spectroradiometer), y posteriormente se explicó su variabilidad en términos de sus principales tributarios. La media mensual de la concentración del MPS mostró, un máximo a partir de fines del verano hasta mediados de otoño, y un mínimo, a partir de mediados del invierno hasta comienzos del verano. El río Bermejo (RBe), es el tributario que más sedimentos en suspensión transporta, situación que se reflejó en la relación significativa hallada entre la concentración media mensual del MPS y la descarga mensual promedio del RBe. La variación estacional del MPS, tuvo valores máximos durante el otoño y el verano, y valores mínimos en el invierno y la primavera, reflejando así el patrón mensual de descarga del RBe con uno y dos meses de retraso. La variación espacial evidenció tres regiones: interior, central y exterior. Por su parte, la variabilidad anual denotó una marcada estacionalidad en el patrón de cobertura espacial de las aguas con mayor concentración de MPS. La distribución de las anomalías estuvo relacionada con la influencia de la descarga de los ríos, lo que puso de manifiesto que el patrón temporal no está vinculado con el ciclo ENSO (El Niño – Sourthen Oscillation). Estos resultados nos permitieron denotar la importancia del RBe (no ENSO dependiente) para explicar el patrón de anomalías del MPS observado en el RdlP.Agradecemos al Dr. Carlos Ángel Lasta y a la Dra. Claudia Gloria Simionato por su ayuda en el campo oceanográfico, a la Dra. Ana Inés Dogliotti en el procesamiento de imágenes. Este trabajo fue financiado en parte por ANPCyT (Agencia Nacional de Investigación Científica y Tecnológica de Argentina) PICT 2010-1831, y por una beca de Doctorado CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas). Contribución INIDEP Nº 2129.Camiolo, MD.; Cozzolino, E.; Jaureguizar, A. (2018). Material Particulado en Suspensión en el Río de la Plata: importancia del río Bermejo en su variabilidad espacio-temporal. Revista de Teledetección. (51):1-18. https://doi.org/10.4995/raet.2018.9864SWORD11851Balay, M. A. 1961. El Río de la Plata entre la atmósfera y el mar. Servicio de Hidrografía Naval. Buenos Aires. 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p53Psi is a transcriptionally inactive p53 isoform able to reprogram cells toward a metastatic-like state

Although much is known about the underlying mechanisms of p53 activity and regulation, the factors that influence the diversity and duration of p53 responses are not well understood. Here we describe a unique mode of p53 regulation involving alternative splicing of the TP53 gene. We found that the use of an alternative 3' splice site in intron 6 generates a unique p53 isoform, dubbed p53Psi. At the molecular level, p53Psi is unable to bind to DNA and does not transactivate canonical p53 target genes. However, like certain p53 gain-of-function mutants, p53Psi attenuates the expression of E-cadherin, induces expression of markers of the epithelial-mesenchymal transition, and enhances the motility and invasive capacity of cells through a unique mechanism involving the regulation of cyclophilin D activity, a component of the mitochondrial inner pore permeability. Hence, we propose that p53Psi encodes a separation-of-function isoform that, although lacking canonical p53 tumor suppressor/transcriptional activities, is able to induce a prometastatic program in a transcriptionally independent manner

GRACy: a tool for analysing human cytomegalovirus sequence data

Modern DNA sequencing has instituted a new era in human cytomegalovirus (HCMV) genomics. A key development has been the ability to determine the genome sequences of HCMV strains directly from clinical material. This involves the application of complex and often non-standardized bioinformatics approaches to analysing data of variable quality in a process that requires substantial manual intervention. To relieve this bottleneck, we have developed GRACy (Genome Reconstruction and Annotation of Cytomegalovirus), an easy-to-use tookit for analysing HCMV sequence data. GRACy automates and integrates modules for read filtering, genotyping, genome assembly, genome annotation, variant analysis and data submission. These modules were tested extensively on simulated and experimental data and outperformed generic approaches. GRACy is written in Python and is embedded in a graphical user interface with all required dependencies installed by a single command. It runs on the Linux operating system, and is designed to allow the future implementation of a cross-platform version. GRACy is distributed under a GPL 3.0 license and is freely available at https://bioinformatics.cvr.ac.uk/software/ with the manual and a test dataset

Whole-genome approach to assessing human cytomegalovirus dynamics in transplant patients undergoing antiviral therapy

Human cytomegalovirus (HCMV) is the most frequent cause of opportunistic viral infection following transplantation. Viral factors of potential clinical importance include the selection of mutants resistant to antiviral drugs and the occurrence of infections involving multiple HCMV strains. These factors are typically addressed by analyzing relevant HCMV genes by PCR and Sanger sequencing, which involves independent assays of limited sensitivity. To assess the dynamics of viral populations with high sensitivity, we applied high-throughput sequencing coupled with HCMV-adapted target enrichment to samples collected longitudinally from 11 transplant recipients (solid organ, n=9, and allogeneic hematopoietic stem cell, n=2). Only the latter presented multiple-strain infections. Four cases presented resistance mutations (n=6), two (A594V and L595S) at high (100%) and four (V715M, 32 V781I, A809V and T838A) at low (<25%) frequency. One allogeneic hematopoietic stem cell transplant recipient presented up to four resistance mutations, each at low frequency. The use of high throughput sequencing to monitor mutations and strain composition in people at risk of HCMV disease is of potential value in helping clinicians implement the most appropriate therapy

Genetic variability, chemotype distribution, and aggressiveness of Fusarium culmorum on durum wheat in Tunisia

Fusarium culmorum is the most commonly reported root rot pathogen in Tunisian durum wheat. Isolates of the pathogen from four durum wheat growing areas in the north of Tunisia were analyzed for their chemotypes. Two chemotypes were detected at unequal abundance (96% of 3-ADON and 4% of NIV). Distribution of a SNP mutation located at the position 34 bp after the first exon of the EF-1\u3b1 partial sequence was analysed, to verify whether the haplotype was specifically associated to Fusarium root rot. A and T haplotypes were homogeneously distributed in three different Tunisian regions (Mateur, Beja and Bousalem) but not for the region of Bizerte, from which greatest number of A haplotype strains were detected. The isolates were tested for their virulence under glasshouse conditions, and a mean of 91% of crown and root infection was observed. Chemotype influenced virulence, but there was no significant influence of the geographical origin or haplotype on virulence. The distribution of three inter simple sequence repeats (ISSR) was examined, to better understand the structure of F. culmorum populations in Tunisia. A total of 27 fragments were obtained with eight polymorphic bands. Cluster analysis showed a high level of similarity between isolates. Analysis of molecular variance confirmed that there was little genetic differentiation among F. culmorum strains from different locations

Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples

Understanding the intrahost evolution of viral populations has implications in pathogenesis, diagnosis and treatment, and has recently made impressive advances from developments in high-throughput sequencing. However, the underlying analyses are very sensitive to sources of bias, error and artefact in the data, and it is important that these are addressed adequately if robust conclusions are to be drawn. The key factors include: (i) determining the number of viral strains present in the sample analysed; (ii) monitoring the extent to which the data represent these strains and assessing the quality of these data; (iii) dealing with the effects of cross-contamination; and (iv) ensuring that the results are reproducible. We investigated these factors by generating sequence datasets, including biological and technical replicates, directly from clinical samples obtained from a small cohort of patients who had been infected congenitally with the herpesvirus human cytomegalovirus, with the aim of developing a strategy for identifying high-confidence intrahost variants. We found that such variants were few in number and typically present in low proportions, and concluded that human cytomegalovirus exhibits a very low level of intrahost variability. In addition to clarifying the situation regarding human cytomegalovirus, our strategy has wider applicability to understanding the intrahost variability of other viruses

Spatial Analyses of Mono, Di and Trinucleotide Trends in Plant Genes

Genomic DNA sequences display compositional heterogeneity on many scales. In this paper we analyzed tendencies and anomalies in the occurence of mono, di and trinucleotides in structural regions of plant genes. Representation of these trends as a function of position along genic sequences highlighted compositional features peculiar of either monocots or eudicots that were remarkably uniform within these two evolutionary clades. The most evident of these features appeared in the form of gradient of base content along the direction of transcription. The robustness of such a representation was validated in sequences sub-datasets generated considering structural and compositional features such as total length of cds, overall GC content and genic orientation in the genome. Piecewise regression analyses indicated that the gradients could be conveniently approximated to a two segmented model where a first region featuring a steep slope is followed by a second segment fitting a milder variation. In general, monocots species showed steeper segments than eudicots. The guanine gradient was the most distinctive feature between the two evolutionary clades, being moderately increasing in eudicots and firmly decreasing in monocots. Single gene investigation revealed that a high proportion of genes show compositional trends compatible with a segmented model suggesting that these features are essential attributes of gene organization. Dinucleotide and trinucleotide biases were referred to expectation based on a random union of the component elements. The average bias at dinucleotide level identified a significant undererpresentation of some dinucleotide and the overrepresention of others. The bias at trinucleotide level was on average low. Finally, the analysis of bryophyte coding sequences showed mononucleotide, dinucleotide and trinucleotide compositional trends resembling those of higher plants. This finding suggested that the emergenge of compositional bias is an ancient event in evolution which was already present at the time of land conquest by green plants

Mutational Biases and Selective Forces Shaping the Structure of Arabidopsis Genes

Recently features of gene expression profiles have been associated with structural parameters of gene sequences in organisms representing a diverse set of taxa. The emerging picture indicates that natural selection, mediated by gene expression profiles, has a significant role in determining genic structures. However the current situation is less clear in plants as the available data indicates that the effect of natural selection mediated by gene expression is very weak. Moreover, the direction of the patterns in plants appears to contradict those observed in animal genomes. In the present work we analized expression data for >18000 Arabidopsis genes retrieved from public datasets obtained with different technologies (MPSS and high density chip arrays) and compared them with gene parameters. Our results show that the impact of natural selection mediated by expression on genes sequences is significant and distinguishable from the effects of regional mutational biases. In addition, we provide evidence that the level and the breadth of gene expression are related in opposite ways to many structural parameters of gene sequences. Higher levels of expression abundance are associated with smaller transcripts, consistent with the need to reduce costs of both transcription and translation. Expression breadth, however, shows a contrasting pattern, i.e. longer genes have higher breadth of expression, possibly to ensure those structural features associated with gene plasticity. Based on these results, we propose that the specific balance between these two selective forces play a significant role in shaping the structure of Arabidopsis genes

Human cytomegalovirus genomes sequenced directly from clinical material: variation, multiple-strain infection, recombination and gene loss

The genomic characteristics of human cytomegalovirus (HCMV) strains sequenced directly from clinical pathology samples were investigated, focusing on variation, multiple-strain infection, recombination, and gene loss. A total of 207 datasets generated in this and previous studies using target enrichment and high-throughput sequencing were analyzed, in the process enabling the determination of genome sequences for 91 strains. Key findings were that (i) it is important to monitor the quality of sequencing libraries in investigating variation; (ii) many recombinant strains have been transmitted during HCMV evolution, and some have apparently survived for thousands of years without further recombination; (iii) mutants with nonfunctional genes (pseudogenes) have been circulating and recombining for long periods and can cause congenital infection and resulting clinical sequelae; and (iv) intrahost variation in single-strain infections is much less than that in multiple-strain infections. Future population-based studies are likely to continue illuminating the evolution, epidemiology, and pathogenesis of HCMV

Human cytomegalovirus RNA2.7 is required for upregulating multiple cellular genes to promote cell motility and viral spread late in lytic infection

Long non-coding RNAs are frequently associated with broad modulation of gene expression and thus provide the cell with the ability to synchronize entire metabolic processes. We used transcriptomic approaches to investigate whether the most abundant human cytomegalovirus-encoded lncRNA, RNA2.7, has this characteristic. By comparing cells infected with wild-type virus (WT) with cells infected with RNA2.7 deletion mutants, RNA2.7 was implicated in regulating a large number of cellular genes late in lytic infection. Pathway analysis indicated that >100 of these genes are associated with promoting cell movement, and the ten most highly regulated of these were validated in further experiments. Morphological analysis and live cell tracking of WT- and RNA2.7 mutant-infected cells indicated that RNA2.7 is involved in promoting the movement and detachment of infected cells late in infection, and plaque assays using sparse cell monolayers indicated that RNA2.7 is also involved in promoting cell-to-cell spread of virus. Consistent with the observation that upregulated mRNAs are relatively A+U-rich, which is a trait associated with transcript instability, and that they are also enriched in motifs associated with mRNA instability, transcriptional inhibition experiments on WT- and RNA2.7 mutant-infected cells showed that four upregulated transcripts were longer-lived in the presence of RNA2.7. These findings demonstrate that RNA2.7 is required for promoting cell movement and viral spread late in infection and suggest that this may be due to general stabilization of A+U-rich transcripts