Biological warfare between two bacterial viruses in a defense archipelago sheds light on the spread of CRISPR-Cas systems.

CRISPR-Cas systems are adaptive immunity systems of bacteria and archaea that prevent infection by viruses and other external mobile genetic elements. It is currently known that these defense systems can be co-opted by the same viruses. We have found one of these viruses in the opportunistic pathogen Acinetobacter baumannii, and the same system has been also found in an integration hotspot of the bacterial genome that harbors other multiple defense systems.

Monosaccharides improve symptoms of an animal model for type III galactosemia, through the activation of the insulin pathway.

Type III galactosemia is characterized by the inability to metabolize galactose due to deficiency of the UDP-galactose-4-epimerase (GALE) gene, which catalyzes the interconversion of UDP-Galactose and UDP-Glucose. Additionally, GALE interconverts UDP-N-Acetylgalactosamine and UDP-N-Acetylglucosamine. These four sugars are needed for glycosylation of biomolecules.

ASACO: Automatic and Serial Analysis of CO-expression to discover gene modifiers with potential use in drug repurposing.

Massive gene expression analyses are widely used to find differentially expressed genes under specific conditions. The results of these experiments are often available in public databases that are undergoing a growth similar to that of molecular sequence databases in the past. This now allows novel secondary computational tools to emerge that use such information to gain new knowledge.

Morphological description and DNA-based association of the last instar larva of Erotesis schachti Malicky 1982 (Trichoptera: Leptoceridae), an endemic of the Iberian Peninsula.

In this paper we describe the main morphological characteristics that distinguish the full-grown larva of Erotesis schachti, an endemic of the Iberian Peninsula. The conspecificity of the larva and adult was confirmed by DNA analysis. Morphological features that easily discriminate it from the similar species Erotesis baltica are given.

Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems.

CRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been associated with the virus they recognize, and it has been named CRISPR dark matter.

E-learning strategies from a bioinformatics postgraduate programme to improve student engagement and completion rate.

Motivation: E-learning is the standard solution adopted in transnational study programmes for which multiple face-to-face learning places are not an option. Bioinformatics is compatible with e-learning because its resource requirements are low. Online learning, however, is usually associated with high dropout rates because students start from a very low computational level and/or they need support to conduct practical analyses on their own.

A Simple Multiplex Reverse Transcription-PCR Method for the Diagnosis of L-A and M Totiviruses in Saccharomyces cerevisiae.

Killer yeasts and their toxins have many potential applications in environmental, medical, and industrial biotechnology. The killer phenotype in Saccharomyces cerevisiae relies on the cytoplasmic persistence of two dsRNA viruses, L-A and M. M encodes the toxin, and L-A provides proteins for expression, replication, and capsids for both viruses.

Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators and co-option of cellular pathways.

Unlabelled: The current genomics era is bringing an unprecedented growth in the amount of gene expression data, only comparable to the exponential growth of sequences in databases during the last decades. This data now allows the design of secondary analyses that take advantage of this information to create new knowledge through specific computational approaches. One of these feasible analyses is the evaluation of the expression level for a gene through a series of different conditions or cell types.

Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators.

The current genomics era is bringing an unprecedented growth in the amount of gene expression data, only comparable to the exponential growth of sequences in databases during the last decades. This data allow the design of secondary analyses that take advantage of this information to create new knowledge. One of these feasible analyses is the evaluation of the expression level for a gene through a series of different conditions or cell types.

CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats.

The genomics era is resulting in the generation of a plethora of biological sequences that are usually stored in public databases. There are many computational tools that facilitate the annotation of these sequences, but sometimes they produce mistakes that enter the databases and can be propagated when erroneous data are used for secondary analyses, such as gene prediction or homology searching. While developing a computational gene finder based on protein-coding sequences, we discovered that the reference UniProtKB protein database is contaminated with some spurious sequences translated from DNA containing clustered regularly interspaced short palindromic repeats.

Cost-Effectiveness of Bariatric Surgery Compared With Nonsurgical Treatment in People With Obesity and Comorbidity in Colombia.

Background: The increase in obesity prevalence and its relationship with multiple cardiovascular complications have raised the burden of obesity in the general population. Bariatric surgery has shown to be more effective in reducing weight than the traditional pharmacologic and nonpharmacologic treatments.

Objective: To evaluate the cost-effectiveness of this alternative compared with standard treatment in the Colombian context.

AnABlast: Re-searching for Protein-Coding Sequences in Genomic Regions.

AnABlast is a computational tool that highlights protein-coding regions within intergenic and intronic DNA sequences which escape detection by standard gene prediction algorithms. DNA sequences with small protein-coding genes or exons, complex intron-containing genes, or degenerated DNA fragments are efficiently targeted by AnABlast. Furthermore, this algorithm is particularly useful in detecting protein-coding sequences with nonsignificant homologs to sequences in databases.

Description of the last instar larva of Stenophylax espanioli Schmid 1957 (Trichoptera: Limnephilidae) from southern Iberian Peninsula with the barcode of the species and synoptic key for identification of the known Stenophylax larvae from the Iberian Peninsula.

The larva of Stenophylax espanioli Schmid 1957 is described, illustrated, and compared with morphologically similar Limnephilidae larvae from the Iberian Peninsula. In addition, the sequence of fragments of the mtCOI gene in the barcode region of two individuals are reported and registered in the GenBank Database. Finally, a synoptic key of the known larvae of Stenophylax species from the Iberian Peninsula is given.

A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors.

Aim: Rescoring of docking-binding poses can significantly improve molecular docking results. Our aim was to evaluate postprocessing docking protocols in order to determine the most suitable methodology for the study of the binding of congeneric compounds to protein kinases.

Materials & Methods: Diverse ligand-receptor poses generated after docking were submitted to different relaxation protocols.

Binding of the anticancer drug BI-2536 to human serum albumin. A spectroscopic and theoretical study.

BI-2536 is a potent Polo-like kinase inhibitor which induces apoptosis in diverse human cancer cell lines. The binding affinity of BI-2536 for human serum albumin (HSA) protein may define its pharmacokinetic and pharmacodynamic profile. We have studied the binding of BI-2536 to HSA by means of different spectroscopic techniques and docking calculations.

Synthesis, characterization, DNA interactions and antiproliferative activity on glioblastoma of iminopyridine platinum(II) chelate complexes.

A series of iminopyridine platinum chelate compounds has been prepared and characterized by NMR spectroscopy and single-crystal X-ray diffraction. The complexes were evaluated in C6 tumoral cells as an in vitro model for glioblastoma multiforme. The DNA-binding properties of these complexes were studied by UV-Vis absorption and fluorescence spectroscopy and Density Functional Theory calculations were performed in an effort to rationalize the observed properties at the molecular level.

DFT study of the effect of fluorine atoms on the crystal structure and semiconducting properties of poly(arylene-ethynylene) derivatives.

The effect of fluorine substitution on the molecular structure, crystal packing, and n-type semiconducting properties of a set of poly(arylene-ethynylene) polymers based on alternating thiadiazole and phenyl units linked through ethynylene groups has been studied by means of Density Functional Theory. As a result, an enlargement in the interplanar distance between cofacial polymer chains, as well as a decrease of the electronic coupling and electron mobility is predicted. On the other hand, fluorination could facilitate electron injection into the material.

Glide Path Management with Single- and Multiple-instrument Rotary Systems in Curved Canals: A Micro-Computed Tomographic Study.

Introduction: Securing a reproducible glide path before instrumentation is recommended to maintain the original geometry of the root canal system and to prevent file separation. Mechanical glide path management systems have been introduced to expedite this step. The aim of this study was to compare apical transportation, canal volume increase, and working time during glide path management with ProGlider (PG; Dentsply Tulsa Dental Specialties, Tulsa, OK) and PathFiles (PF, Dentsply Tulsa Dental Specialties).

Spectroscopic study on binding of gentisic acid to bovine serum albumin.

The interaction of (gentisic acid) GA with (bovine serum albumin) BSA has been studied by different spectroscopic techniques. GA is a monoanionic specie at the working pH of 7.4, it was determined by combining UV-Vis absorption spectroscopy and theoretical calculations.

Theoretical estimation of the optical bandgap in a series of poly(aryl-ethynylene)s: a DFT study.

Aimed to optimize the ratio accuracy/computational cost, in this work we study the performance of three different theoretical methodologies in the calculation of the optical bandgap for a test set made of a number of poly(aryl-ethynylene)s related polymers. Infinite, ideal polymer chains were first optimized by means of periodic calculations. Different length oligomers were afterward generated by direct replication of the corresponding periodic structure and their optical bandgaps were calculated by means of different time dependent-density functional theory (TD-DFT) methodologies.

Escherichia coli carbon source metabolism affects longevity of its predator Caenorhabditis elegans.

Nutrition is probably the most determinant factor affecting aging. Microorganisms of the intestinal flora lay in the interface between available nutrients and nutrients that are finally absorbed by multicellular organisms. They participate in the processing and transformation of these nutrients in a symbiotic or commensalistic relationship.

Mechanistic and kinetic study on the reactions of coumaric acids with reactive oxygen species: a DFT approach.

The mechanism and kinetics of reactions between coumaric acids and a series of reactive oxygen species ((•)OX) was studied through the density functional theory (DFT). H atom abstraction from -OH and -COOH groups and addition to the nonaromatic double bond were the most representative reaction pathways chosen for which free energy barriers and rate constants were calculated within the transition state theory (TST) framework. From these calculations, it was estimated that (•)OH > (•)OCH3 > (•)OOH > (•)OOCH3 is the order of reactivity of (•)OX with any coumaric acid.

Mutational analysis of the P1 phosphorylation domain in Escherichia coli CheA, the signaling kinase for chemotaxis.

The histidine autokinase CheA functions as the central processing unit in the Escherichia coli chemotaxis signaling machinery. CheA receives autophosphorylation control inputs from chemoreceptors and in turn regulates the flux of signaling phosphates to the CheY and CheB response regulator proteins. Phospho-CheY changes the direction of flagellar rotation; phospho-CheB covalently modifies receptor molecules during sensory adaptation.