Computational Prediction and Experimental Assessment of Secreted/Surface Proteins from Mycobacterium tuberculosis H37Rv

The mycobacterial cell envelope has been implicated in the pathogenicity of tuberculosis and therefore has been a prime target for the identification and characterization of surface proteins with potential application in drug and vaccine development. In this study, the genome of Mycobacterium tuberculosis H37Rv was screened using Machine Learning tools that included feature-based predictors, general localizers and transmembrane topology predictors to identify proteins that are potentially secreted to the surface of M. tuberculosis, or to the extracellular milieu through different secretory pathways. The subcellular localization of a set of 8 hypothetically secreted/surface candidate proteins was experimentally assessed by cellular fractionation and immunoelectron microscopy (IEM) to determine the reliability of the computational methodology proposed here, using 4 secreted/surface proteins with experimental confirmation as positive controls and 2 cytoplasmic proteins as negative controls. Subcellular fractionation and IEM studies provided evidence that the candidate proteins Rv0403c, Rv3630, Rv1022, Rv0835, Rv0361 and Rv0178 are secreted either to the mycobacterial surface or to the extracellular milieu. Surface localization was also confirmed for the positive controls, whereas negative controls were located on the cytoplasm. Based on statistical learning methods, we obtained computational subcellular localization predictions that were experimentally assessed and allowed us to construct a computational protocol with experimental support that allowed us to identify a new set of secreted/surface proteins as potential vaccine candidates.     

Suitability of flow cytometry for estimating bacterial biovolume in natural plankton samples: comparison with microscopy data

The relationship between flow cytometry data and epifluorescence microscopy measurements was assessed in bacterioplankton samples from 80 lakes to estimate bacterial biovolume and cell size distribution. The total counts of 4',6'-diamidino-2-phenylindole-stained cells estimated by both methods were significantly related, and the slope of their linear regression was not significantly different from 1, indicating that both methods produce very similar estimates of bacterial abundance. The relationships between side scatter (SSC) and 4',6'-diamidino-2-phenylindole fluorescence and cell volume (microscopy values) were improved by binning of the data in three frequency classes for each, but further increases in the number of classes did not improve these relationships. Side scatter was the best cell volume predictor, and significant relationships were observed between the SSC classes and the smallest (R2 = 0.545, P < 0.001, n = 80) and the largest (R2 = 0.544, P < 0.001, n = 80) microscopy bacterial-size classes. Based on these relationships, a reliable bacterial biomass estimation was obtained from the SSC frequency classes. Our study indicates that flow cytometry can be used to properly estimate bacterioplankton biovolume, with an accuracy similar to those of more time-consuming microscopy methods.     

Late Hauterivian coralline algae (Rhodophyta,Corallinales) from the Iberian Chain (E Spain). Taxonomy and the evolution of multisporangial reproductive structures

Upper Hauterivian reefal carbonates of the Llàcova Formation (Maestrat Basin, Iberian Chain, E Spain) contain Sporolithon phylloideum (Bucur and Dragastan) Tomás, Aguirre, Braga and Martín-Closas comb. nov. and Sporolithon rude (Lemoine) Ghosh and Maithy (1996). Moussavian et al. (1993) identified them as Parakymalithon phylloideum (Bucur and Dragastan) Moussavian 1987 and Archaeolithothamnium rude Lemoine 1925. The re-assessment of the type of P. phylloideum and additional material indicate that the diagnostic characters of the genus do not warrant separation from Sporolithon and the new combination Sporolithon phylloideum is proposed. The lectotype of Sporolithon rude presents sporangial cavities grouped in sori that can be merged originating a structure that resembles the multiporate tetrasporangial conceptacles of the Hapalidiaceae. We hypothesize that multiporate tetrasporangial conceptacles could have originated from the fusion of several sporangial cavities, suggesting a phylogenetic linkage between Sporolithaceae and Hapalidiaceae supported by other anatomical features, molecular phylogeny and the fossil record.     

Spondylitis in a humpback whale (Megaptera novaeangliae) from the southeast Pacific

A 7.25 m long male humpback whale (Megaptera novaeangliae) with spondylitis was found beached on August 13, 1994 at Ancon, Ecuador (2 degrees 23' S, 80 degrees 47' W). The condition involved at least 11 vertebrae, 7 lumbar (L4 to L11) and 4 caudal (Ca1 to Ca4). Partial fusion of vertebrae was observed as a result of intervertebral bony proliferation, likely impeding full motion. The relatively young age of this specimen and the severity of the deformities suggest an infectious, rather than degenerative, process. The gross findings are most consistent with some type of spondyloarthritis. Although this condition has previously been identified in a number of cetacean species, the pathogenesis, population impact and ecologic implications have not been fully assessed. This is the third case described for humpback whales and the first for a humpback whale from the SE Pacific.     

The CK1 gene family: expression patterning in zebrafish development

Protein kinase CK1 is a ser/thr protein kinase family which has been identified in the cytosol cell fraction, associated with membranes as well as in the nucleus. Several isoforms of this gene family have been described in various organisms: CK1alpha, CK1beta, CK1delta, CK1epsilon and CK1gamma. Over the last decade, several members of this family have been involved in development processes related to wnt and sonic hedgehog signalling pathways. However, there is no detailed temporal information on the CK1 family in embryonic stages, even though orthologous genes have been described in several different vertebrate species. In this study, we describe for the first time the cloning and detailed expression pattern of five CK1 zebrafish genes. Sequence analysis revealed that zebrafish CK1 proteins are highly homologous to other vertebrate orthologues. Zebrafish CK1 genes are expressed throughout development in common and different territories. All the genes studied in development show maternal and zygotic expression with the exception of CK1epsilon. This last gene presents only a zygotic component of expression. In early stages of development CK1 genes are ubiquitously expressed with the exception of CK1epsilon. In later stages the five CK1 genes are expressed in the brain but not in the same way. This observation probably implicates the CK1 family genes in different and also in redundant functions. This is the first time that a detailed comparison of the expression of CK1 family genes is directly assessed in a vertebrate system throughout development.     

Zonobiomes, zonoecotones and azonal vegetation along the Pacific coast of North America

In this study of the Pacific coast of North America, from Baja California to Alaska, we evaluated the hypothesis that the floristic composition of azonal vegetation determines areas and distribution limits similar to those of the corresponding zonobiomes (ZB), and does so in response to the same macroclimatic changes occurring on the continental scale. To this end, 686 vascular plants of the different habitats found in 279 sites along this coastal strip were recorded. Using an objective classification system (Average Linkage Clustering) and factorial analysis, floristic data acquired in fieldwork were classified into groups, which were in turn related to regional macroclimates. Our main finding was that the azonal coastal vegetation follows a distribution model that is closely linked to the corresponding macroclimate. The four ZB of the northern Pacific coast show a flora and azonal vegetation characteristic to each zonobiome; the latitudinal limits of the azonal vegetation practically coinciding with those already established for the zonal vegetation. The Boreal and Temperate ZB show high percentages of broadly distributed elements. The floristically richest zonobiome in terms of endemic taxa is the Mediterranean zonobiome, whereas the flora of Baja California is characterized by a high number of taxa related to Neotropical flora, especially to those showing links with South America. Data on the geographical distribution and habitats of the 247 most significant coastal species are also provided.     

Diversity of cultivable bacteria from deep-sea sediments of the Colombian Caribbean and their potential in bioremediation

The diversity of deep-sea cultivable bacteria was studied in seven sediment samples of the Colombian Caribbean. Three hundred and fifty two marine bacteria were isolated according to its distinct morphological character on the solid media, then DNA sequences of the 16S rRNA were amplified to identify the isolated strains. The identified bacterial were arranged in three phylogenetic groups, Firmicutes, Proteobacteria, and Actinobacteria, with 34 different OTUs defined at ≥?97% of similarity and 70 OTUs at ≥?98.65%, being the 51% Firmicutes, 34% Proteobacteria and 15% Actinobacteria. Bacillus and Fictibacillus were the dominant genera in Firmicutes, Halomonas and Pseudomonas in Proteobacteria and Streptomyces and Micromonospora in Actinobacteria. In addition, the strains were tested for biosurfactants and lipolytic enzymes production, with 120 biosurfactant producing strains (mainly Firmicutes) and, 56 lipolytic enzymes producing strains (Proteobacteria). This report contributes to the understanding of the diversity of the marine deep-sea cultivable bacteria from the Colombian Caribbean, and their potential application as bioremediation agents.

     

Loss of MT1‐MMP causes cell senescence and nuclear defects which can be reversed by retinoic acid

MT1-MMP (MMP14) is a collagenolytic enzyme located at the cell surface and implicated in extracellular matrix (ECM) remodeling. Mmp14^−/− mice present dwarfism, bone abnormalities, and premature death. We demonstrate herein that the loss of MT1-MMP also causes cardiac defects and severe metabolic changes, and alters the cytoskeleton and the nuclear lamina structure. Moreover, the absence of MT1-MMP induces a senescent phenotype characterized by up-regulation of p16^INK4a and p21^CIP1/WAF1, increased activity of senescence-associated β-galactosidase, generation of a senescence-associated secretory phenotype, and somatotroph axis alterations. Consistent with the role of retinoic acid signaling in nuclear lamina stabilization, treatment of Mmp14^−/− mice with all-trans retinoic acid reversed the nuclear lamina alterations, partially rescued the cell senescence phenotypes, ameliorated the pathological defects in bone, skin, and heart, and extended their life span. These results demonstrate that nuclear architecture and cell senescence can be modulated by a membrane protease, in a process involving the ECM as a key regulator of nuclear stiffness under cell stress conditions.     

Retraction: ‘Are European birds leaving traditional wintering grounds in the Mediterranean?’, by José Luis Tellería, Álvaro Ramírez and José Ignacio Aguirre

The above article, published online on 20 January 2015 in Wiley Online Library ( wileyonlinelibrary.com ), has been retracted by agreement between the authors, the journal Editors in Chief, Thomas Alerstam and Jan‐Åke Nilsson, the Nordic Society Oikos and John Wiley and Sons Ltd. The aim of this study was to answer the question, ‘Are European birds leaving traditional wintering grounds in the Mediterranean?’ Due to an analytical error the study only analysed EURING circumstance 20 ring records (see the EURING exchange code) which excludes birds hunted by shot and other ways, but not all hunted individuals. As a result, the effect of illegal hunting on ring recoveries was not controlled for in the analyses. This means that the data is affected by ring records from birds other than ‘alive and probably healthy and released by ringer’ (condition 8 in the EURING exchange code). The authors' intention always was to include both condition 8 and circumstance 20, but unfortunately this was not the case. When the data was reanalysed including both condition 8 and circumstance 20 recoveries, there is no longer any support for the main conclusion of the paper and the authors can only conclude that winter ring recoveries in Spain of some common passerines (robin, chiffchaff and blackcap) do not decrease. The authors apologise for this mistake and hope that the retraction will serve to prevent the spread of the unsound conclusions derived from this paper.