Preference for medium dense grass tussocks byHippodamia convergens [Col.: Coccinellidae]

The preference in the choice of hibernacula of the convergent lady beetle,Hippodamia convergens Guérin-Meneville, was investigated with regard to morphological aspects of 2 introduced range grasses,Panicum coloratum (L.), andEragrostis curvula (Schrad.) Beetles strongly preferred tussocks with a ratio in the range of 1.0–3.0 stems per cm² for lovegrass. Preference for klein grass tussocks ranging from 110–130 stems/clump was found. No preference was shown for a particular tussock circumference. It was demonstrated that tussocks could successfully be designated as suitable for beetle aggregation.     

FELLA: an R package to enrich metabolomics data

Background

Pathway enrichment techniques are useful for understanding experimental metabolomics data. Their purpose is to give context to the affected metabolites in terms of the prior knowledge contained in metabolic pathways. However, the interpretation of a prioritized pathway list is still challenging, as pathways show overlap and cross talk effects.

Results

We introduce FELLA, an R package to perform a network-based enrichment of a list of affected metabolites. FELLA builds a hierarchical representation of an organism biochemistry from the Kyoto Encyclopedia of Genes and Genomes (KEGG), containing pathways, modules, enzymes, reactions and metabolites. In addition to providing a list of pathways, FELLA reports intermediate entities (modules, enzymes, reactions) that link the input metabolites to them. This sheds light on pathway cross talk and potential enzymes or metabolites as targets for the condition under study. FELLA has been applied to six public datasets –three from Homo sapiens, two from Danio rerio and one from Mus musculus– and has reproduced findings from the original studies and from independent literature.

Conclusions

The R package FELLA offers an innovative enrichment concept starting from a list of metabolites, based on a knowledge graph representation of the KEGG database that focuses on interpretability. Besides reporting a list of pathways, FELLA suggests intermediate entities that are of interest per se. Its usefulness has been shown at several molecular levels on six public datasets, including human and animal models. The user can run the enrichment analysis through a simple interactive graphical interface or programmatically. FELLA is publicly available in Bioconductor under the GPL-3 license.

     

Golgi study of the anterior dorsal ventricular ridge in a lizard. II. Neuronal cytodifferentiation

The development of the morphologic features of neurons in the anterior dorsal ventricular ridge (ADVR) has been followed in Golgi preparations from the lizard Gallotia galloti between embryonic stage 32 and post-eclosion stages of specimens 3.6–4.5 cm in length. The differentiation sequence of multipolar and bitufted neurons was established. Dendritic growth cones are present after stage 34. Filiform dendritic processes are replaced later on by spines. Clusters of neurons first appear at stage 39 in the periventricular zone, the cells becoming Golgi-impregnated in pairs. After hatching, the number of impregnated cells per cluster increases.     

Role of the renal nerves in blood pressure in male and female SHR

Female spontaneously hypertensive rats (SHR) have lower blood pressures than males. The renin-angiotensin system plays an important role in the sexual dimorphism of blood pressure in SHR. The sympathetic nervous system can stimulate renin release, and, therefore, the present study was performed to determine whether the renal sympathetic nerves play a role in the sexual dimorphism of blood pressure in SHR. Male and female SHR underwent bilateral kidney denervation or sham surgery, and, 2 wk later, mean arterial pressure (MAP) and pulse interval were recorded, and baroreflex sensitivity (BRS) was measured by the sequence technique. Left ventricle index (LVI) was also calculated. MAP was higher in sham-operated males than females (182 +/- 5 vs. 169 +/- 4 mmHg; P < 0.01), but, despite the higher MAP in males, LVI was significantly greater in female rats. BRS was not different between sham-operated male and female SHR. Following bilateral renal denervation, MAP was decreased by a similar percentage (8-10%) in males (169 +/- 2 mmHg) and females (152 +/- 3 mmHg), whereas LVI was reduced only in female SHR. BRS was not altered by renal denervation in either sex. These data indicate that renal nerves play a role in the control of blood pressure in SHR independent of sex, but do not play a role in mediating the sex differences in blood pressure.     

Detection of noncovalent complexes in biological samples by intensity fading and high-mass detection MALDI-TOF mass spectrometry

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry has not yet contributed widely to the study of intact noncovalent biomolecular complexes, because MALDI is known to cause dissociation of the interaction partners and induce formation of nonspecific aggregates. Here, we present a new strategy to circumvent this problem. It is based on intensity fading (in the low m/z range) and high-mass detection MALDI mass spectrometry (MS), using a cryodetector (in the high m/z range), with and without chemical cross-linking of the interaction partners. The study focuses on noncovalent interactions between the human enzyme carboxypeptidase A (hCPA) and three protease inhibitors (PCI, TCI, and LCI) present in heterogeneous mixtures of other nonbinding molecules derived from a biological source, an extract from leech (Hirudo medicinalis). Another example involves an extract of the sea anemone Stichodactyla helianthus, which is used without previous fractionation to detect the specific complex between the enzyme trypsin and the endogenous SphI-1 inhibitor. The results give insight into the mechanism of intensity fading MS and demonstrate that the specificity of binding is greatly favored when the overall concentrations of the analytes (nonbinding molecules, protease inhibitor and target enzyme) present in a biological sample of interest are kept at low concentrations, in the sub-micromolar range. Higher concentrations may lead to unspecific interactions and the formation of aggregates both during the MALDI process and during reaction with the cross-linking reagents. This strategy is expected to advance the field of high-throughput affinity-based approaches, by taking advantage of a new generation of high mass detectors for MALDI-TOF instruments.     

Morphological and functional characterization of beige mouse adrenomedullary secretory vesicles

We tested whether the giant secretory granules observed in the mast cells of the naturally occurring mutant beige mouse (BM) (C57BL/6N-bg) were also present in the adrenal chromaffin cells. The presence of large chromaffin granules (CG) would be a valuable tool for the study of exocytosis in neuronal tissues. Conversely, the observation of large vesicles within chromaffin cells that are different from CG could indicate that CG are of a different origin than granules of mast cells. Ultrastructural analysis demonstrated the presence of large lysososmal-like vesicles in the BM, and also a discrete increase in the number of CG with diameters larger than 240 nm but not of giant CG. In addition, amperometric measurements of single-event exocytosis, using carbon fiber microelectrodes, showed no differences between the quantal size of secretory events from BM and wildtype or bovine chromaffin cells. Minor but significant differences were found between the kinetics of exocytosis in BM cells andwild-type mouse cells. We conclude that CG, but not the abnormal-sized vesicles found in BM chromaffin cells contribute to the catecholamine secretion and that abnormal secretory granules are not present in adrenergic cell lineage.     

Detection of non-covalent protein interactions by 'intensity fading' MALDI-TOF mass spectrometry: applications to proteases and protease inhibitors

Among the main objectives of biomedical and proteomic research is to identify non-covalent interactions involving proteins. Here we provide a detailed protocol to apply matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry for such a purpose using proteases and protease inhibitors in complex biological samples. Our methodology is based on monitoring the reduction in intensity of inhibitors' mass spectrometric signals when their protease target is added to the MALDI sample. The versatility of the protocol permits the target to be added in a soluble form (direct protocol) or immobilized form (indirect protocol). The 'intensity fading' phenomenon is greatly favored when the binding assay is carried out in the sub-micromolar range and the interacting partners occur in mixtures of non-binding compounds. This protocol can be completed in 10 h, taking 20 or 30 min per sample to perform the mass spectrometric data acquisition, depending on whether a soluble or an immobilized target is used.     

Restriction site‐associated DNA sequencing,genotyping error estimation and de novo assembly optimization for population genetic inference

Restriction site‐associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single‐nucleotide polymorphisms. As an empirical example, we use a double‐digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high‐altitude mountains in Mexico.     

The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming

Metabolism is vital to every aspect of cell function, yet the metabolome of induced pluripotent stem cells (iPSCs) remains largely unexplored. Here we report, using an untargeted metabolomics approach, that human iPSCs share a pluripotent metabolomic signature with embryonic stem cells (ESCs) that is distinct from their parental cells, and that is characterized by changes in metabolites involved in cellular respiration. Examination of cellular bioenergetics corroborated with our metabolomic analysis, and demonstrated that somatic cells convert from an oxidative state to a glycolytic state in pluripotency. Interestingly, the bioenergetics of various somatic cells correlated with their reprogramming efficiencies. We further identified metabolites that differ between iPSCs and ESCs, which revealed novel metabolic pathways that play a critical role in regulating somatic cell reprogramming. Our findings are the first to globally analyze the metabolome of iPSCs, and provide mechanistic insight into a new layer of regulation involved in inducing pluripotency, and in evaluating iPSC and ESC equivalence.