Search results for " Spa"
showing 10 items of 6738 documents
Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data
2016
Next-generation sequencing technologies have led to the sequencing of more and more genomes, propelling related research into the era of big data. In this paper, we present ParaBWT, a parallelized Burrows-Wheeler transform (BWT) and suffix array construction algorithm for big genome data. In ParaBWT, we have investigated a progressive construction approach to constructing the BWT of single genome sequences in linear space complexity, but with a small constant factor. This approach has been further parallelized using multi-threading based on a master-slave coprocessing model. After gaining the BWT, the suffix array is constructed in a memory-efficient manner. The performance of ParaBWT has b…
Yeast thioredoxin reductase Trr1p controls TORC1-regulated processes
2018
The thioredoxin system plays a predominant role in the control of cellular redox status. Thioredoxin reductase fuels the system with reducing power in the form of NADPH. The TORC1 complex promotes growth and protein synthesis when nutrients, particularly amino acids, are abundant. It also represses catabolic processes, like autophagy, which are activated during starvation. We analyzed the impact of yeast cytosolic thioredoxin reductase TRR1 deletion under different environmental conditions. It shortens chronological life span and reduces growth in grape juice fermentation. TRR1 deletion has a global impact on metabolism during fermentation. As expected, it reduces oxidative stress tolerance…
Long-term genomic coevolution of host-parasite interaction in the natural environment
2017
Antagonistic coevolution of parasite infectivity and host resistance may alter the biological functionality of species, yet these dynamics in nature are still poorly understood. Here we show the molecular details of a long-term phage–bacterium arms race in the environment. Bacteria (Flavobacterium columnare) are generally resistant to phages from the past and susceptible to phages isolated in years after bacterial isolation. Bacterial resistance selects for increased phage infectivity and host range, which is also associated with expansion of phage genome size. We identified two CRISPR loci in the bacterial host: a type II-C locus and a type VI-B locus. While maintaining a core set of conse…
Anatomy and physiology of cisternostomy
2016
Cisternostomy is defined as opening the basal cisterns to atmospheric pressure. This technique helps to reduce the intracranial pressure in severe head trauma as well as other conditions when the so-called sudden “brain swelling” troubles the surgeon. We elaborated the surgical anatomy of this procedure as well as the proposed physiology of how cisternostomy works. This novel technique may change the current trends in neurosurgery.
Intra-tumour heterogeneity of diffuse large B-cell lymphoma involves the induction of diversified stroma-tumour interfaces
2020
Abstract Background Intra-tumour heterogeneity in lymphoid malignancies encompasses selection of genetic events and epigenetic regulation of transcriptional programs. Clonal-related neoplastic cell populations are unsteadily subjected to immune editing and metabolic adaptations within different tissue microenvironments. How tissue-specific mesenchymal cells impact on the diversification of aggressive lymphoma clones is still unknown. Methods Combining in situ quantitative immunophenotypical analyses and RNA sequencing we investigated the intra-tumour heterogeneity and the specific mesenchymal modifications that are associated with A20 diffuse large B-cell lymphoma (DLBCL) cells seeding of d…
Extracellular Superoxide Dismutase Expression in Papillary Thyroid Cancer Mesenchymal Stem/Stromal Cells Modulates Cancer Cell Growth and Migration
2017
AbstractTumor stroma-secreted growth factors, cytokines, and reactive oxygen species (ROS) influence tumor development from early stages to the metastasis phase. Previous studies have demonstrated downregulation of ROS-producing extracellular superoxide dismutase (SOD3) in thyroid cancer cell lines although according to recent data, the expression of SOD3 at physiological levels stimulates normal and cancer cell proliferation. Therefore, to analyze the expression of SOD3 in tumor stroma, we characterized stromal cells from the thyroid. We report mutually exclusive desmoplasia and inflammation in papillary and follicular thyroid cancers and the presence of multipotent mesenchymal stem/stroma…
Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family
2017
AbstractWe introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the …
Fungal community assemblage of different soil compartments in mangrove ecosystem
2017
AbstractThe fungal communities of different soil compartments in mangrove ecosystem are poorly studied. We sequenced the internal transcribed spacer (ITS) regions to characterize the fungal communities in Avicennia marina root-associated soils (rhizosphere and pneumatophore) and bulk soil compartments. The rhizosphere but not pneumatophore soil compartment had significantly lower fungal species richness than bulk soil. However, bulk soil fungal diversity (Shannon diversity index) was significantly higher than both pneumatophore and rhizosphere soil compartments. The different soil compartments significantly affected the fungal community composition. Pairwise sample analyses showed that bulk…
Transcranial random noise stimulation over the primary motor cortex in PD-MCI patients: a crossover, randomized, sham-controlled study
2020
AbstractMild cognitive impairment (MCI) is a very common non-motor feature of Parkinson’s disease (PD) and the non-amnestic single-domain is the most frequent subtype. Transcranial random noise stimulation (tRNS) is a non-invasive technique, which is capable of enhancing cortical excitability. As the main contributor to voluntary movement control, the primary motor cortex (M1) has been recently reported to be involved in higher cognitive functioning. The aim of this study is to evaluate the effects of tRNS applied over M1 in PD-MCI patients in cognitive and motor tasks. Ten PD-MCI patients, diagnosed according to the Movement Disorder Society, Level II criteria for MCI, underwent active (re…
Microwear and isotopic analyses on cave bear remains from Toll Cave reveal both short-term and long-term dietary habits
2019
Dietary habits of the extinct Ursus spelaeus have always been a controversial topic in paleontological studies. In this work, we investigate carbon and nitrogen values in the bone collagen and dental microwear of U. spelaeus specimens recovered in Level 4 from Toll Cave (Moia, Catalonia, NE Iberian Peninsula). These remains have been dated to > 49,000 C-14 BP. The ability of both proxies to provide data on the diet of U. spelaeus at different times in the life-history (isotopes: average diet of life; microwear: last days/weeks before death), allows us to generate high-resolution and complementary data. Our results show lower values (delta C-13 & delta N-15) in cave bears than in strict herb…