Diaphragm adaptations in patients with COPD

Inspiratory muscle weakness in patients with COPD is of major clinical relevance. For instance, maximum inspiratory pressure generation is an independent determinant of survival in severe COPD. Traditionally, inspiratory muscle weakness has been ascribed to hyperinflation-induced diaphragm shortening. However, more recently, invasive evaluation of diaphragm contractile function, structure, and biochemistry demonstrated that cellular and molecular alterations occur, of which several can be considered pathologic of nature. Whereas the fiber type shift towards oxidative type I fibers in COPD diaphragm is regarded beneficial, rendering the overloaded diaphragm more resistant to fatigue, the reduction of diaphragm fiber force generation in vitro likely contributes to diaphragm weakness. The reduced diaphragm force generation at single fiber level is associated with loss of myosin content in these fibers. Moreover, the diaphragm in COPD is exposed to oxidative stress and sarcomeric injury. This review postulates that the oxidative stress and sarcomeric injury activate proteolytic machinery, leading to contractile protein wasting and, consequently, loss of force generating capacity of diaphragm fibers in patients with COPD. Interestingly, several of these presumed pathologic alterations are already present early in the course of the disease (GOLD I/II), although these patients appear not limited in their daily life activities. Treatment of diaphragm dysfunction in COPD is complex since its etiology is unclear, but recent findings indicate the ubiquitin-proteasome pathway as a prime target to attenuate diaphragm wasting in COPD.     

Development of new nuclear markers and characterization of single nucleotide polymorphisms in kelp gull (Larus dominicanus)

The present study seeks to develop nuclear markers for the kelp gull (Larus dominicanus). We hereby report the characterization of 12 independent nuclear introns, where 104 single nucleotide polymorphisms (SNPs) in 8138 sequenced base pairs were observed. These SNP markers are the first to be designed for genotyping a gull species. The markers will provide useful tools for understanding which processes act or acted upon kelp gulls to cause their low genetic variability in mitochondrial DNA. In addition, these markers open a new opportunity for population genetic and evolutionary studies in the Laridae group.     

Thermal welding of biological tissues derived from porcine aorta for manufacturing bioprosthetic cardiac valves

Sutures in cardiac valve bioprostheses have several disadvantages as they have to be manually processed and the suturing region is always a mechanically weak spot. Thermal welding of biological tissues has been evaluated as a means of replacing sutures by the direct application of heat to tissues. The mechanical strength of the welds increased up to 50°C and with lower degrees of humidity and longer times of welding. Chemical fixation was essential for the stability of the weld during re-hydration. The average mechanical strength of the welds (0.87 MPa) was lower than the strength of sutures (1.36 MPa) but some results showed strengths that were similar to sutures. Raman and electron micrographs showed that weld formation is primarily associated with chemical bonds between collagen fibers rather than chain flow and interpenetration.     

Influence of moon phase on fish assemblages in estuarine mangrove tidal creeks

Significant differences in the composition of fish assemblages during different moon phases were detected in mangrove tidal creeks of the Goiana Estuary. The numbers of Zabaleta anchovy Anchovia clupeoides, Tarpon snook Centropomus pectinatus and Guavina Guavina guavina as well as at least 15 other species showed significant changes according to moon phase and were higher in terms of individuals (32%) and mass (34%) during the new moon.     

Identification of a Napin-Like Peptide from Eugenia malaccensis L. Seeds with Inhibitory Activity Toward Staphylococcus aureus and Salmonella Enteritidis

This study aimed to purify and characterize peptides from the seeds of Eugenia malaccensis, L. (jambo) with inhibitory activity against the foodborne pathogens Staphylococcus aureus and Salmonella Enteritidis. Crude extract (CE), precipitate fraction 30–60 % and molecules between 3.5 and 10 kDa obtained from precipitate fraction 30–60 % (Em2) showed inhibitory activity against the tested bacterial strains. The highest antibacterial activity was observed for Em2 against S. aureus. The major peak eluted at approximately 30 % in an acetonitrile gradient in reverse-phase chromatography of Em2 (Em2-F1 to Em2-F19), and it showed the highest antibacterial activity, which was twofold higher against S. aureus than against S. Enteritidis. MALDI-ToF spectra of Em2-F18 revealed a molecular mass of 1,231.1 Da and the amino acid sequence showed high identity to the napin family. These findings report for the first time a napin-like peptide from E. malaccensis L. seeds with potential to be applied as a new anti-Staphylococcus molecule.     

Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Pasteurella pneumotropica Evades the Human Complement System by Acquisition of the Complement Regulators Factor H and C4BP

Pasteurella pneumotropica is an opportunist Gram negative bacterium responsible for rodent pasteurellosis that affects upper respiratory, reproductive and digestive tracts of mammals. In animal care facilities the presence of P. pneumotropica causes severe to lethal infection in immunodeficient mice, being also a potential source for human contamination. Indeed, occupational exposure is one of the main causes of human infection by P. pneumotropica. The clinical presentation of the disease includes subcutaneous abscesses, respiratory tract colonization and systemic infections. Given the ability of P. pneumotropica to fully disseminate in the organism, it is quite relevant to study the role of the complement system to control the infection as well as the possible evasion mechanisms involved in bacterial survival. Here, we show for the first time that P. pneumotropica is able to survive the bactericidal activity of the human complement system. We observed that host regulatory complement C4BP and Factor H bind to the surface of P. pneumotropica, controlling the activation pathways regulating the formation and maintenance of C3-convertases. These results show that P. pneumotropica has evolved mechanisms to evade the human complement system that may increase the efficiency by which this pathogen is able to gain access to and colonize inner tissues where it may cause severe infections.     

Defaunation impacts on seed survival and its effect on the biomass of future tropical forests

Large animal species, which provide important ecological functions such as dispersal of seeds or top–down control of seed predators, are very vulnerable in fragmented forests, being unable to survive in small fragments, and facing increasing hunting pressure. The loss of large animals affects two main ecological processes crucial for the tree reproductive cycle: seed dispersal of large seeds (e.g. provided by tapirs) and control of seed predator population (e.g. provided by large cats). The changes in both processes are expected to increase seed mortality since seeds are not dispersed away from conspecifics (causing increased pre‐dispersal mortality due to negative density dependent effects) and/or face increased predation after a dispersal event (post‐dispersal mortality). Although an extensive body of empirical knowledge exists on seed predation, the link between seed loss and adult tree community composition and structure is not well established, as well as the temporal scale seed changes affect adults. Using an individual‐based forest model (FORMIND), we evaluate the long‐term consequences of increased pre and post‐dispersal seed mortality on the future forest biomass retention of a Brazilian northeastern Atlantic forest. Our results show that forest biomass is significantly affected after 80–93% pre‐dispersal loss of large seeds, or post‐dispersal predation densities of 20–25 predators per parent tree. Large‐seeded tree species are at increased risk of local extinction causing up to 26.2% loss of forest biomass when both pre and post‐dispersal processes are combined. However, these changes can last up to 100 years after the occurrence of defaunation. In summary we conclude that large animal loss has the potential to reduce future forest biomass and tree species‐richness by impacting seed survival, and should be considered in the planning of biodiversity friendly landscapes as well as in calculations of the global carbon budget.