Pervasive sign epistasis between conjugative plasmids and drug-resistance chromosomal mutations

Multidrug-resistant bacteria arise mostly by the accumulation of plasmids and chromosomal mutations. Typically, these resistant determinants are costly to the bacterial cell. Yet, recently, it has been found that, in Escherichia coli bacterial cells, a mutation conferring resistance to an antibiotic can be advantageous to the bacterial cell if another antibiotic-resistance mutation is already present, a phenomenon called sign epistasis. Here we study the interaction between antibiotic-resistance chromosomal mutations and conjugative (i.e., self-transmissible) plasmids and find many cases of sign epistasis (40%)--including one of reciprocal sign epistasis where the strain carrying both resistance determinants is fitter than the two strains carrying only one of the determinants. This implies that the acquisition of an additional resistance plasmid or of a resistance mutation often increases the fitness of a bacterial strain already resistant to antibiotics. We further show that there is an overall antagonistic interaction between mutations and plasmids (52%). These results further complicate expectations of resistance reversal by interdiction of antibiotic use.     

Development of a reversed phase high performance liquid chromatography method based on the use of cyclodextrins as mobile phase additives to determine pterostilbene in blueberries

In this work, a reversed phase high performance liquid chromatography (RP-HPLC) method was developed for the determination of pterostilbene in food samples. The novel method is based on the addition of cyclodextrins (CDs) to the mobile phase where the complexation of pterostilbene by CDs is carried out. In order to select the most suitable conditions for the RP-HPLC method, the effect of several physico-chemical parameters on the complexation of pterostilbene by CDs was studied. Our results show that the addition of 12 mM HP-β-CD to a 50:50 (v/v) methanol:water mobile phase at 25°C and pH 7.0 significantly improves the main analytical parameters. In addition, it was seen that pterostilbene forms a 1:1 complex with HP-β-CD, showing an apparent complexation constant of 251±13 M(-1). Finally, in order to study the validity of the proposed method, blueberries were analyzed and the concentration of pterostilbene has been determined.     

Phytosterols and phytosterolemia: gene–diet interactions

Phytosterol intake is recommended as an adjunctive therapy for hypercholesterolemia, and plant sterols/stanols can reduce cholesterol absorption at the intestinal lumen through the Niemann-Pick C1 Like 1 (NPC1L1) transporter pathway by competitive solubilization in mixed micelles. Phytosterol absorption is of less magnitude than cholesterol and is preferably secreted in the intestinal lumen by ABCG5/G8 transporters. Therefore, plasma levels of plant sterols/stanols are negligible compared with cholesterol, under an ordinary diet. The mechanisms of cholesterol and plant sterols absorption and the whole-body pool of sterols are discussed in this chapter. There is controversy about treatment with statins inducing further increase in plasma non-cholesterol sterols raising concerns about the safety of supplementation of plant sterols to such drugs. In addition, increase in plant sterols has also been reported upon consumption of plant sterol-enriched foods, regardless of other treatments. Rare mutations on ABCG5/G8 transporters affecting cholesterol/non-cholesterol extrusion, causing sitosterolemia with xanthomas and premature atheroslerotic disease are now known, and cholesterol/plant sterols absorption inhibitor, ezetimibe, emerges as the drug that reduces phytosterolemia and promotes xanthoma regression. On the other hand, common polymorphisms affecting the NPC1L1 transporter can interfere with the action of ezetimibe. Gene-diet interactions participate in this intricate network modulating the expression of genetic variants on specific phenotypes and can also affect the individual response to the hypolipidemic treatment. These very interesting aspects promoted a great deal of research in the field.     

A blind circadian clock in cavefish reveals that opsins mediate peripheral clock photoreception

The circadian clock is synchronized with the day-night cycle primarily by light. Fish represent fascinating models for deciphering the light input pathway to the vertebrate clock since fish cell clocks are regulated by direct light exposure. Here we have performed a comparative, functional analysis of the circadian clock involving the zebrafish that is normally exposed to the day-night cycle and a cavefish species that has evolved in perpetual darkness. Our results reveal that the cavefish retains a food-entrainable clock that oscillates with an infradian period. Importantly, however, this clock is not regulated by light. This comparative study pinpoints the two extra-retinal photoreceptors Melanopsin (Opn4m2) and TMT-opsin as essential upstream elements of the peripheral clock light input pathway.     

Phylogeography, genetic structure, and gene flow in the endemic freshwater shrimp Palaemonetes suttkusi from Cuatro Ci��negas, Mexico

The valley of Cuatro Ciénegas in Mexico has the highest degree of local endemicity of any habitat in North America. A large number of endemic aquatic species occur both in the Cuatro Ciénegas basin and in the upper parts of the Río Salado de los Nadadores drainage, located immediately to the east of the valley. No natural surface flow occurs between these basins but artificial canals connect both areas. It is not clear whether the sharing of endemics between the Cuatro Ciénegas basin and the Río Salado is due to migration through canals. We conducted a phylogeographic study of mitochondrial haplotypes of the endemic shrimp Palaemonetes suttkusi to determine the evolutionary distinctiveness of the population found in Río Salado. We discovered that P. suttkusi likely has occurred naturally in both basins well into the distant past. Based on molecular clock analyses of the COI gene, the populations in the Río Salado and much of the Cuatro Ciénegas basin likely began diverging from each other between 1.9 and 11.2 Myr ago. The general levels of divergence are substantial but our results suggest there has also likely been recent gene flow between these basins. This is consistent with migration through human-made canals, but also consistent with the occurrence of natural gene flow during intermittent wet periods in the past million years. We also found significant differentiation of the Pozas Azules area from the rest of the Cuatro Ciénegas basin, a finding that is concordant with several phylogeographic studies on other aquatic endemics in Cuatro Ciénegas. We recommend that the upper parts of the Río Salado, the Pozas Azules area, and the rest of the Cuatro Ciénegas basin should each be considered independent evolutionarily significant units for conservation, and that migration of species through human-made canals should be monitored and controlled.     

Abdominal muscle activation changes if the purpose is to control pelvis motion or thorax motion

The aim of this study was to compare trunk muscular recruitment and lumbar spine kinematics when motion was constrained to either the thorax or the pelvis. Nine healthy women performed four upright standing planar movements (rotations, anterior–posterior translations, medial–lateral translations, and horizontal circles) while constraining pelvis motion and moving the thorax or moving the pelvis while minimizing thorax motion, and four isometric trunk exercises (conventional curl-up, reverse curl-up, cross curl-up, and reverse cross curl-up). Surface EMG (upper and lower rectus abdominis, lateral and medial aspects of external oblique, internal oblique, and latissimus dorsi) and 3D lumbar displacements were recorded. Pelvis movements produced higher EMG amplitudes of the oblique abdominals than thorax motions in most trials, and larger lumbar displacements in the medial–lateral translations and horizontal circles. Conversely, thorax movements produced larger rotational lumbar displacement than pelvis motions during rotations and higher EMG amplitudes for latissimus dorsi during rotations and anterior–posterior translations and for lower rectus abdominis during the crossed curl-ups. Thus, different neuromuscular compartments appear when the objective changes from pelvis to thorax motion. This would suggest that both movement patterns should be considered when planning spine stabilization programs, to optimize exercises for the movement and muscle activations desired.     

Plastid analysis of pigmented undifferentiated cells of marigold <Emphasis Type="Italic">Tagetes erecta</Emphasis> L. by transmission electron microscopy

Marigold (Tagetes erecta) flowers are primarily used in industry for their high pigment content. Flower color development implies that chloroplast–chromoplast transition is associated with carotenoid biosynthesis. We report the recovery of undifferentiated pigmented marigold cells, various callus tissues, and their analysis by transmission electron microscopy in order to observe accumulating pigment and development of subcellular structures. Callus was generated from leaf explants and after several rounds of recurrent selection. Green-, yellow-, and brown-colored callus were obtained that showed distinct carotenoid profiles. For green material, violaxanthin, lutein, zeaxanthin, and β-carotene were produced, while yellow callus generated mainly lutein, as did the brown callus. Chloroplast–chromoplast transition was followed by measuring plastid size and shape in undifferentiated marigold cells by digital image analysis. Cellular alterations were evident in brown callus. Chloroplasts were the main structure in green callus, while yellow callus clearly showed the formation of plastoglobules, structures that are correlated with chloroplast–chromoplast transition. The high number of plastoglobules observed in yellow callus is possibly directly related to pigment synthesis and accumulation.     

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.