Development versus predation: Transcriptomic changes during the lifecycle of Myxococcus xanthus

Myxococcus xanthus is a multicellular bacterium with a complex lifecycle. It is a soil-dwelling predator that preys on a wide variety of microorganisms by using a group and collaborative epibiotic strategy. In the absence of nutrients this myxobacterium enters in a unique developmental program by using sophisticated and complex regulatory systems where more than 1,400 genes are transcriptional regulated to guide the community to aggregate into macroscopic fruiting bodies filled of environmentally resistant myxospores. Herein, we analyze the predatosome of M. xanthus, that is, the transcriptomic changes that the predator undergoes when encounters a prey. This study has been carried out using as a prey Sinorhizobium meliloti, a nitrogen fixing bacteria very important for the fertility of soils. The transcriptional changes include upregulation of genes that help the cells to detect, kill, lyse, and consume the prey, but also downregulation of genes not required for the predatory process. Our results have shown that, as expected, many genes encoding hydrolytic enzymes and enzymes involved in biosynthesis of secondary metabolites increase their expression levels. Moreover, it has been found that the predator modifies its lipid composition and overproduces siderophores to take up iron. Comparison with developmental transcriptome reveals that M. xanthus downregulates the expression of a significant number of genes coding for regulatory elements, many of which have been demonstrated to be key elements during development. This study shows for the first time a global view of the M. xanthus lifecycle from a transcriptome perspective.Grant PID2020-112634GB-I0 funded by MCIN/AEI/ 10.13039/501100011033FEDER funds (grant A-BIO-126-UGR20

A Highly Available Cluster of Web Servers with Increased Storage Capacity

Ponencias de las Decimoséptimas Jornadas de Paralelismo de la Universidad de Castilla-La Mancha celebradas el 18,19 y 20 de septiembre de 2006 en AlbaceteWeb servers scalability has been traditionally solved by improving software elements or increasing hardware resources of the server machine. Another approach has been the usage of distributed architectures. In such architectures, usually, file al- location strategy has been either full replication or full distribution. In previous works we have showed that partial replication offers a good balance between storage capacity and reliability. It offers much higher storage capacity while reliability may be kept at an equivalent level of that from fully replicated solutions. In this paper we present the architectural details of Web cluster solutions adapted to partial replication. We also show that partial replication does not imply a penalty in performance over classical fully replicated architectures. For evaluation purposes we have used a simulation model under the OMNeT++ framework and we use mean service time as a performance comparison metric.Publicad

Sand size variability inside the hopper of a trailing suction dredger in regards to beach nourishment projects

Amongst the design parameters for a beach nourishment project, sand size must be highlighted. Sand size is critical not only to compare the suitability of a borrow sand to substitute the eroded native sand, but also to identify the new equilibrium beach profile and to calculate the sediment volume necessary to achieve the projected berm or beach width. Some researchers have already taken into account the phenomena that change the theoretical volume of sand needed for a beach nourishment project (CUR, 1987; CEM 2002) such as the methodology for the hopper measurements taken on board of the dredger (Muñoz-Perez et al., 2003) or the sand porosity variability (Roman-Sierra et al., 2014). Nevertheless, no investigation has been carried out about the variability of sand size inside the hopper of a trailing suction dredger till nowadays. There are several reasons to justify this possible heterogeneity of the granulometric parameters inside the hopper. Firstly, there is the intrinsic variability of the sediment characteristics at the sea bottom. On top of that, most of the vessels which dredge nowadays are of the Trailing Suction Hopper Dredgers (TSHD) type and this means that these vessels do not dredge in a stationary way, i.e. at a certain location and vicinity, but along a big stretch of the bottom. Moreover, the fall speed of sand depends directly on the grain diameter (for a given density); i.e. the larger the grain sizes the faster the grain deposits and so, probably, the coarser grains would be at the bottom of the hopper and the finer grains would be at the top. Finally, it is noteworthy a word about the fragments of shells or bioclasts: because of their flat shape, these pieces linger more than the silica grains to decant and, therefore, their percentage will most likely be larger at the surface of the hopper

Metal-responsive RNA polymerase extracytoplasmic function (ECF) sigma factors

In order to survive, bacteria must adapt to multiple fluctuations in their environment, including coping with changes in metal concentrations. Many metals are essential for viability, since they act as cofactors of indispensable enzymes. But on the other hand, they are potentially toxic because they generate reactive oxygen species or displace other metals from proteins, turning them inactive. This dual effect of metals forces cells to maintain homeostasis using a variety of systems to import and export them. These systems are usually inducible, and their expression is regulated by metal sensors and signal-transduction mechanisms, one of which is mediated by extracytoplasmic function (ECF) sigma factors. In this review, we have focused on the metalresponsive ECF sigma factors, several of which are activated by iron depletion (FecI, FpvI and PvdS), while others are activated by excess of metals such as nickel and cobalt (CnrH), copper (CarQ and CorE) or cadmium and zinc (CorE2). We focus particularly on their physiological roles, mechanisms of action and signal transduction pathways.This work has been supported by the Spanish Government, grant BFU2016-75425-P to Aurelio Moraleda-Muñoz (70% funded by FEDER)

Mechanisms of Action of Non-Canonical ECF Sigma Factors

Extracytoplasmic function (ECF) sigma factors are subunits of the RNA polymerase specialized in activating the transcription of a subset of genes responding to a specific environmental condition. The signal-transduction pathways where they participate can be activated by diverse mechanisms. The most common mechanism involves the action of a membrane-bound anti-sigma factor, which sequesters the ECF sigma factor, and releases it after the stimulus is sensed. However, despite most of these systems following this canonical regulation, there are many ECF sigma factors exhibiting a non-canonical regulatory mechanism. In this review, we aim to provide an updated and comprehensive view of the different activation mechanisms known for non-canonical ECF sigma factors, detailing their inclusion to the different phylogenetic groups and describing the mechanisms of regulation of some of their representative members such as EcfG from Rhodobacter sphaeroides, showing a partner-switch mechanism; EcfP from Vibrio parahaemolyticus, with a phosphorylation-dependent mechanism; or CorE from Myxococcus xanthus, regulated by a metal-sensing C-terminal extension.Spanish Government (PID2020-112634GB-I00)FEDER funds (grant A-BIO-126-UGR20

Influence of Di erent Sieving Methods on Estimation of Sand Size Parameters

Sieving is one of the most used operational methods to determine sand size parameters which are essential to analyze coastal dynamics. However, the influence of hand versus mechanical shaking methods has not yet been studied. Herein, samples were taken from inside the hopper of a trailing suction dredger and sieved by hand with sieves of 10 and 20 cm diameters on board the dredger. Afterwards, these same samples were sieved with a mechanical shaker in the laboratory on land. The results showed di erences for the main size parameters D50, standard deviation, skewness, and kurtosis. Amongst the main results, it should be noted that the highest values for D50 and kurtosis were given by the small sieves method. On the other hand, the lowest values were given by the mechanical shaker method in the laboratory. Furthermore, standard deviation and skewness did not seem to be a ected by the sieving method which means that all the grainsize distribution was shifted but the shape remained unchanged. The few samples that do not follow these patterns have a higher percentage of shells. Finally and definitely, the small sieves should be rejected as a sieving method aboard

Malware similarity and a new fuzzy hash: Compound Code Block Hash (CCBHash)

In the last few years, malware analysis has become increasingly important due to the rise of sophisticated cyberattacks. One of the objectives of this cybersecurity branch is to find similarities between different files or functions used by malware programmers, thus allowing malware detection, classification and even attribution in a timely manner. In this article we survey the state of the art in this area, reviewing the different techniques that can be applied to the field, with the objective of studying similarity, and therefore detecting, classifying and attributing malware samples. We have developed a fuzzy hash capable of characterizing malware by generating an easily comparable and storable signature of its functions. Since our goal is to detect these similarities in huge amounts of data within a reasonable time-frame, the size of the hash must be limited while retaining as much information as possible.Funding for open access charge: Universidad de Málaga / CBU

Soil erosion susceptibility assessment in Mediterranean areas through the analysis of soil quality. A test in the Guadalmedina watershed (Málaga, Spain).

Soil erosion is one of the most relevant environmental problems facing society today. Thus, climate change has a direct impact on these processes through a feedback loop, especially in the Mediterranean region, where the situation is conceived as one of maximum fragility and sensitivity. The increase in extreme precipitation and temperature events, together with differential human land use, lead to an intense impoverishment of Mediterranean soils. In this sense, it is essential to determine the levels of susceptibility of the territory to erosive processes in order to create strategies aimed at improving the management of the territory and reducing the possible existing risks. Specifically, this work has focused on the Guadalmedina river basin in the province of Malaga (Spain), which is representative of the current dynamics of the Mediterranean landscape. To achieve this, a soil quality index based on a multi-criteria analysis of different soil indicators (water, physical and organic) has been applied in this work, using a total of 132 soil samples. In addition, the results of this analysis have been compared with soil erosion values derived from the application of the RUSLE model. On a general level, lower soil erosion rates clearly correspond to those areas where soil quality indicators show optimal values. Likewise, the results obtained show how soil organic indicators play a decisive role in water erosion processes in the Mediterranean area.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Eribulin mesylate as a microtubule inhibitor for treatment of patients with metastatic breast cancer

Metastatic breast cancer (MBC) remains an incurable disease, with the goals of care aimed at maximizing the patient’s duration and quality of life. Treatment options for MBC have become more efficacious and numerous. In addition to endocrine and chemotherapy agents, a number of targeted agents, including trastuzumab and bevacizumab, have further enhanced the landscape of therapeutic options. Eribulin mesylate (E7389) is a nontaxane microtubule dynamics inhibitor, and a structurally simplified synthetic analog of the natural marine product, halichondrin B, with a novel mechanism of action that has shown antitumor activity in pretreated MBC. Eribulin has shown a manageable tolerability profile in Phase I–II clinical trials and an improvement in overall survival compared with treatment of physician’s choice, without relevant toxicities in a recently published Phase III trial. This review will focus on eribulin as a new active agent for MBC and its role in the management of breast disease

In depth analysis of the mechanism of action of metal-dependent sigma factors: characterization of CorE2 from Myxococcus xanthus

Extracytoplasmic function sigma factors represent the third pillar of signal-transduction mechanisms in bacteria. The variety of stimuli they recognize and mechanisms of action they use have allowed their classification into more than 50 groups. We have characterized CorE2 from Myxococcus xanthus, which belongs to group ECF44 and upregulates the expression of two genes when it is activated by cadmium and zinc. Sigma factors of this group contain a Cys-rich domain (CRD) at the C terminus which is essential for detecting metals. Point mutations at the six Cys residues of the CRD have revealed the contribution of each residue to CorE2 activity. Some of them are essential, while others are either dispensable or their mutations only slightly affect the activity of the protein. However, importantly, mutation of Cys174 completely shifts the specificity of CorE2 from cadmium to copper, indicating that the Cys arrangement of the CRD determines the metal specificity. Moreover, the conserved CxC motif located between the sigma2 domain and the sigma4.2 region has also been found to be essential for activity. The results presented here contribute to our understanding of the mechanism of action of metal-dependent sigma factors and help to define new common features of the members of this group of regulators.Spanish Government [CSD2009-00006, BFU2012-33248, 70% funded by FEDER]. Funding for open access charge: Grupo BIO318, Junta de Andalucía