A Retrospective View of Software Maintenance and Reengineering Research.

As a summary of past, current, and future trends in software maintenance and reengineering research, we give in this editorial a retrospective look from the past 14 years to now. We provide insight on how software maintenance has evolved and on the most important research topics presented in the series of the European Conference on Software Maintenance and Reengineering.

Inoculum sources and Preservation in Soils of Phytophthora parasitica from Cherry Tomato in Continental Crop Areas in Southeast Spain

Inoculum sources and Preservation in Soils of Phytophthora parasitica from Cherry Tomato in Continental Crop Areas in Southeast Spain

Reviewing technical approaches for sharing and preservation of experimental data

Empirical Software Engineering (ESE) replication researchers need to store and manipulate experimental data for several purposes, in particular analysis and reporting. Current research needs call for sharing and preservation of experimental data as well. In a previous work, we analyzed Replication Data Management (RDM) needs. A novel concept, called Experimental Ecosystem, was proposed to solve current deficiencies in RDMapproaches. The empirical ecosystem provides replication researchers with a common framework that integrates transparently local heterogeneous data sources. A typical situation where the Empirical Ecosystem is applicable, is when several members of a research group, or several research groups collaborating together, need to share and access each other experimental results. However, to be able to apply the Empirical Ecosystem concept and deliver all promised benefits, it is necessary to analyze the software architectures and tools that can properly support it.

Balancing management and preservation of mediterranean scattered oak woodlands (Dehesas) in human-dominated landscapes

Los sistemas agroforestales mediterráneos tienen una gran importancia ecológica y socioeconómica, y mantienen altos valores medioambientales y de diversidad biológica a la vez que producen importantes servicios ecosistémicos. Estos sistemas han sido testigos de diversos cambios rápidos y drásticos en su gestión y aprovechamiento durante el último siglo. La mayor parte de la investigación desarrollada en esta tesis doctoral ha sido llevada a cabo en las dehesas españolas. Esta tesis nos muestra: i) la evidencia de la existencia de un cambio global del estrato arbóreo y del manejo del pastoreo en el todo el área de distribución de la dehesa durante los últimos 60 años; ii) la importancia del papel que juega el arbolado disperso y el adecuado manejo del ganado en la mejora de la producción, calidad y diversidad de las comunidades herbáceas, que a su vez, un pasto herbáceo bien desarrollado es importante para la rentabilidad del sistema, evaluando estos efectos bajo distintos escenarios de clima y calidad de estación; y iii) la evidencia de la falta de regeneración en sistemas agroforestales mediterráneos bajo distintos tipos de manejo del pastoreo, y además se evalúa el crecimiento y desarrollo de las pocas plántulas existentes que serán las que aseguren la viabilidad y persistencia y de estos sistemas. El arbolado disperso de estos sistemas ha experimentado una reducción importante en su densidad arbórea y fracción de cabida cubierta durante el periodo entre 1950-1980 donde tuvieron lugar importantes transformaciones en la actividad agropecuaria. La cabaña ganadera de ovino disminuyó drásticamente en los años 70 en comparación a la de bovino que desde entonces ha aumentado progresivamente hasta la actualidad. Por otro lado, el mismo tipo de manejo del ganado doméstico (especialmente bovino) durante bastante tiempo (mínimo 30 años) provocó una reducción significativa de la densidad de las plántulas. Además la probabilidad de ocurrencia y la intensidad de daños por herbivoría fue mayor bajo pastoreo bovino (con daños más intensos y consistentes) que bajo pastoreo ovino o sin pastoreo doméstico (presencia de ciervos). También el patrón de crecimiento de las plantas jóvenes estuvo afectado por el tipo de manejo, generando plántulas achaparradas en el caso del bovino y plántulas esbeltas favoreciendo el crecimiento en altura en el caso del ovino. La presencia de un arbolado disperso generó una mayor diversidad y variación en la producción de las comunidades herbáceas según las condiciones de disponibilidad de agua. Especialmente, el ecotono como microhábitat sostuvo altos valores de diversidad herbácea. La presencia del ganado bajo pastoreo continuo de intensidad moderada a alta, especialmente el bovino, incrementó los rendimientos de producción y diversidad del estrato herbáceo. Los resultados de esta tesis nos muestran la importancia que tiene la existencia de un equilibrio entre la producción y la conservación de los sistemas agroforestales mediterráneos para obtener una producción sostenible de servicios ecosistémicos mientras se asegura la perpetuación del sistema a largo plazo. Es crucial diseñar planes de gestión incorporando objetivos de conservación que integren técnicas silvopastorales apropiadas para poder aplicar en los sistemas agroforestales mediterráneos. ABSTRACT Mediterranean scattered oak woodlands have great ecological and socio-economic importance, supporting high environmental and amenity values, and relatively rich biological diversity while producing important ecosystem services. They have been witnesses of different and fast changes developed in the last century. Most of the research developed in this dissertation has conducted within dehesas. This thesis provides: i) the global change evidence of the tree layer and grazing management experienced in the land-use range of a Mediterranean scattered oak woodland (dehesa) over the last 60 years; ii) the important role of scattered trees and adequate management grazing in the improvement of grassland yield, quality and diversity - which it is important, in turn, for the system profitability - under different climate scenarios and site quality; and iii) the lack of oak regeneration evidence under some given representative management regimes and how is the growth development of these plants to assure the viability and persistence of Mediterranean scattered oak woodlands. Tree layer experienced a significant reduction in dehesas during 1950-1980 period where the highest human impacts took place. Sheep herd decreased drastically during the 1970s and, in contrast, cattle have been increasing gradually since then. On the other hand, same livestock grazing management (especially cattle) during long time (minimum 30 years) within Mediterranean scattered oak woodlands reduced strongly the density of young oak plants and showed high probability of herbivory occurrence and intensity. Young plant growth pattern was greatly modified by livestock. Cattle grazing generated stunted plants and sheep grazing generated slender plants favoring the height growth. Microsites created by large trees modified the herbaceous yield according the water availability of the year and generated high plant diversity within herbaceous communities. Especially, ecotone microsite supported high values of herbaceous diversity. The presence of livestock species increased the herbaceous yield and maintained a more diverse community under continuous grazing at both moderate and high intensities; especially cattle. Thus, around the influence of scattered trees there is a high amount of different interactions among livestock, trees and grasslands maintaining and enhancing the quality of whole dehesa system. The results of this thesis highlight how important is balancing management and preservation of Mediterranean scattered oak woodlands to obtain the optimum ecosystem services while the system conservation is assured for a long-term. It is crucial to design management plans with conservation goals that include appropriate silvopastoral practices in Mediterranean scattered oak woodlands.

Balancing management and preservation of mediterranean scattered oak woodlands (Dehesas) in human-dominated landscapes

Los sistemas agroforestales mediterráneos tienen una gran importancia ecológica y socioeconómica, y mantienen altos valores medioambientales y de diversidad biológica a la vez que producen importantes servicios ecosistémicos. Estos sistemas han sido testigos de diversos cambios rápidos y drásticos en su gestión y aprovechamiento durante el último siglo. La mayor parte de la investigación desarrollada en esta tesis doctoral ha sido llevada a cabo en las dehesas españolas. Esta tesis nos muestra: i) la evidencia de la existencia de un cambio global del estrato arbóreo y del manejo del pastoreo en el todo el área de distribución de la dehesa durante los últimos 60 años; ii) la importancia del papel que juega el arbolado disperso y el adecuado manejo del ganado en la mejora de la producción, calidad y diversidad de las comunidades herbáceas, que a su vez, un pasto herbáceo bien desarrollado es importante para la rentabilidad del sistema, evaluando estos efectos bajo distintos escenarios de clima y calidad de estación; y iii) la evidencia de la falta de regeneración en sistemas agroforestales mediterráneos bajo distintos tipos de manejo del pastoreo, y además se evalúa el crecimiento y desarrollo de las pocas plántulas existentes que serán las que aseguren la viabilidad y persistencia y de estos sistemas. El arbolado disperso de estos sistemas ha experimentado una reducción importante en su densidad arbórea y fracción de cabida cubierta durante el periodo entre 1950-1980 donde tuvieron lugar importantes transformaciones en la actividad agropecuaria. La cabaña ganadera de ovino disminuyó drásticamente en los años 70 en comparación a la de bovino que desde entonces ha aumentado progresivamente hasta la actualidad. Por otro lado, el mismo tipo de manejo del ganado doméstico (especialmente bovino) durante bastante tiempo (mínimo 30 años) provocó una reducción significativa de la densidad de las plántulas. Además la probabilidad de ocurrencia y la intensidad de daños por herbivoría fue mayor bajo pastoreo bovino (con daños más intensos y consistentes) que bajo pastoreo ovino o sin pastoreo doméstico (presencia de ciervos). También el patrón de crecimiento de las plantas jóvenes estuvo afectado por el tipo de manejo, generando plántulas achaparradas en el caso del bovino y plántulas esbeltas favoreciendo el crecimiento en altura en el caso del ovino. La presencia de un arbolado disperso generó una mayor diversidad y variación en la producción de las comunidades herbáceas según las condiciones de disponibilidad de agua. Especialmente, el ecotono como microhábitat sostuvo altos valores de diversidad herbácea. La presencia del ganado bajo pastoreo continuo de intensidad moderada a alta, especialmente el bovino, incrementó los rendimientos de producción y diversidad del estrato herbáceo. Los resultados de esta tesis nos muestran la importancia que tiene la existencia de un equilibrio entre la producción y la conservación de los sistemas agroforestales mediterráneos para obtener una producción sostenible de servicios ecosistémicos mientras se asegura la perpetuación del sistema a largo plazo. Es crucial diseñar planes de gestión incorporando objetivos de conservación que integren técnicas silvopastorales apropiadas para poder aplicar en los sistemas agroforestales mediterráneos. ABSTRACT Mediterranean scattered oak woodlands have great ecological and socio-economic importance, supporting high environmental and amenity values, and relatively rich biological diversity while producing important ecosystem services. They have been witnesses of different and fast changes developed in the last century. Most of the research developed in this dissertation has conducted within dehesas. This thesis provides: i) the global change evidence of the tree layer and grazing management experienced in the land-use range of a Mediterranean scattered oak woodland (dehesa) over the last 60 years; ii) the important role of scattered trees and adequate management grazing in the improvement of grassland yield, quality and diversity - which it is important, in turn, for the system profitability - under different climate scenarios and site quality; and iii) the lack of oak regeneration evidence under some given representative management regimes and how is the growth development of these plants to assure the viability and persistence of Mediterranean scattered oak woodlands. Tree layer experienced a significant reduction in dehesas during 1950-1980 period where the highest human impacts took place. Sheep herd decreased drastically during the 1970s and, in contrast, cattle have been increasing gradually since then. On the other hand, same livestock grazing management (especially cattle) during long time (minimum 30 years) within Mediterranean scattered oak woodlands reduced strongly the density of young oak plants and showed high probability of herbivory occurrence and intensity. Young plant growth pattern was greatly modified by livestock. Cattle grazing generated stunted plants and sheep grazing generated slender plants favoring the height growth. Microsites created by large trees modified the herbaceous yield according the water availability of the year and generated high plant diversity within herbaceous communities. Especially, ecotone microsite supported high values of herbaceous diversity. The presence of livestock species increased the herbaceous yield and maintained a more diverse community under continuous grazing at both moderate and high intensities; especially cattle. Thus, around the influence of scattered trees there is a high amount of different interactions among livestock, trees and grasslands maintaining and enhancing the quality of whole dehesa system. The results of this thesis highlight how important is balancing management and preservation of Mediterranean scattered oak woodlands to obtain the optimum ecosystem services while the system conservation is assured for a long-term. It is crucial to design management plans with conservation goals that include appropriate silvopastoral practices in Mediterranean scattered oak woodlands.

Dissociation among in vitro telomerase activity, telomere maintenance, and cellular immortalization

The immortalization of human cells is a critical step during tumorigenesis. In vitro, normal human somatic cells must overcome two proliferative blockades, senescence and crisis, to become immortal. Transformation with viral oncogenes extends the life span of human cells beyond senescence. Such transformed cells eventually succumb to crisis, a period of widespread cellular death that has been proposed to be the result of telomeric shortening. We now show that ectopic expression of the telomerase catalytic subunit (human telomerase reverse transcriptase or hTERT) and subsequent activation of telomerase can allow postsenescent cells to proliferate beyond crisis, the last known proliferative blockade to cellular immortality. Moreover, we demonstrate that alteration of the carboxyl terminus of human telomerase reverse transcriptase does not affect telomerase enzymatic activity but impedes the ability of this enzyme to maintain telomeres. Telomerase-positive cells expressing this mutant enzyme fail to undergo immortalization, further tightening the connection between telomere maintenance and immortalization.

Restriction-modification gene complexes as selfish gene entities: Roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion

We have reported some type II restriction-modification (RM) gene complexes on plasmids resist displacement by an incompatible plasmid through postsegregational host killing. Such selfish behavior may have contributed to the spread and maintenance of RM systems. Here we analyze the role of regulatory genes (C), often found linked to RM gene complexes, in their interaction with the host and the other RM gene complexes. We identified the C gene of EcoRV as a positive regulator of restriction. A C mutation eliminated postsegregational killing by EcoRV. The C system has been proposed to allow establishment of RM systems in new hosts by delaying the appearance of restriction activity. Consistent with this proposal, bacteria preexpressing ecoRVC were transformed at a reduced efficiency by plasmids carrying the EcoRV RM gene complex. Cells carrying the BamHI RM gene complex were transformed at a reduced efficiency by a plasmid carrying a PvuII RM gene complex, which shares the same C specificity. The reduction most likely was caused by chromosome cleavage at unmodified PvuII sites by prematurely expressed PvuII restriction enzyme. Therefore, association of the C genes of the same specificity with RM gene complexes of different sequence specificities can confer on a resident RM gene complex the capacity to abort establishment of a second, incoming RM gene complex. This phenomenon, termed “apoptotic mutual exclusion,” is reminiscent of suicidal defense against virus infection programmed by other selfish elements. pvuIIC and bamHIC genes define one incompatibility group of exclusion whereas ecoRVC gene defines another.

Telomerase expression and activity are coupled with myocyte proliferation and preservation of telomeric length in the failing heart

The role and even the existence of myocyte proliferation in the adult heart remain controversial. Documentation of cell cycle regulators, DNA synthesis, and mitotic images has not modified the view that myocardial growth can only occur from hypertrophy of an irreplaceable population of differentiated myocytes. To improve understanding the biology of the heart and obtain supportive evidence of myocyte replication, three indices of cell proliferation were analyzed in dogs affected by a progressive deterioration of cardiac performance and dilated cardiomyopathy. The magnitude of cycling myocytes was evaluated by the expression of Ki67 in nuclei. Ki67 labeling of left ventricular myocytes increased 5-fold, 12-fold, and 17-fold with the onset of moderate and severe ventricular dysfunction and overt failure, respectively. Telomerase activity in vivo is present only in multiplying cells; this enzyme increased 2.4-fold and 3.1-fold in the decompensated heart, preserving telomeric length in myocytes. The contribution of cycling myocytes to telomerase activity was determined by the colocalization of Ki67 and telomerase in myocyte nuclei. More than 50% of Ki67-positive cells expressed telomerase in the overloaded myocardium, suggesting that these myocytes were the morphological counterpart of the biochemical assay of enzyme activity. Moreover, we report that 20–30% of canine myocytes were telomerase competent, and this value was not changed by cardiac failure. In conclusion, the enhanced expression of Ki67 and telomerase activity, in combination with Ki67-telomerase labeling of myocyte nuclei, support the notion that myocyte proliferation contributes to cardiac hypertrophy of the diseased heart.

Cdc45p assembles into a complex with Cdc46p/Mcm5p, is required for minichromosome maintenance, and is essential for chromosomal DNA replication.

We report the isolation and characterization of CDC45, which encodes a polypeptide of 650 amino acids that is essential for the initiation of chromosomal DNA replication in the budding yeast, Saccharomyces cerevisiae. CDC45 genetically interacts with at least two members of the MCM (minichromosome maintenance) family of replication genes, CDC46 and CDC47, which are proposed to perform a role in restricting initiation of DNA replication to once per cell cycle. Like mutants in several MCM genes, alleles of CDC45 also show a severe minichromosome maintenance defect. Together, these observations imply that Cdc45p performs a role in the control of initiation events at chromosomal replication origins. We investigated this possibility further and present evidence demonstrating that Cdc45p is assembled into complexes with one MCM family member, Cdc46p/Mcm5p. These observations point to a role for Cdc45p in controlling the early steps of chromosomal DNA replication in conjunction with MCM polypeptide complexes. Unlike the MCMs, however, the subcellular localization of Cdc45p does not vary with the cell cycle, making it likely that Cdc45p interacts with MCMs only during the nuclear phase of MCM localization in G1.