An expanded auxin-inducible degron toolkit for Caenorhabditis elegans

The auxin-inducible degron (AID) system has emerged as a powerful tool to conditionally deplete proteins in a range of organisms and cell types. Here, we describe a toolkit to augment the use of the AID system in Caenorhabditis elegans. We have generated a set of single-copy, tissue-specific (germline, intestine, neuron, muscle, pharynx, hypodermis, seam cell, anchor cell) and pan-somatic TIR1-expressing strains carrying a co-expressed blue fluorescent reporter to enable use of both red and green channels in experiments. These transgenes are inserted into commonly used, well-characterized genetic loci. We confirmed that our TIR1-expressing strains produce the expected depletion phenotype for several nuclear and cytoplasmic AID-tagged endogenous substrates. We have also constructed a set of plasmids for constructing repair templates to generate fluorescent protein::AID fusions through CRISPR/Cas9-mediated genome editing. These plasmids are compatible with commonly used genome editing approaches in the C. elegans community (Gibson or SapTrap assembly of plasmid repair templates or PCR-derived linear repair templates). Together these reagents will complement existing TIR1 strains and facilitate rapid and high-throughput fluorescent protein::AID tagging of genes. This battery of new TIR1-expressing strains and modular, efficient cloning vectors serves as a platform for straightforward assembly of CRISPR/Cas9 repair templates for conditional protein depletion.     

Assessing the trophic ecology of three sympatric squid in the marine ecosystem off the Patagonian Shelf by combining stomach content and stable isotopic analyses

Squid species are important components of the Southern Atlantic Ocean ecosystems, as they prey on a wide range of crustaceans, fish and cephalopods. As a result of this trophic interaction and their high abundance, they are considered reliable indicators of energy transfer and biomass in the food web. We identified Illex argentinus, Doryteuthis gahi and Onykia ingens as the most important squid species interacting on the Patagonian shelf, and used isotope analysis and stomach content identification to assess the feeding ecology and interaction of these squids in the ecosystem. Our results describe trophic interactions by direct predation of O. ingens and I. argentinus on D. gahi, and a trophic overlap of the three squid, and indicate a higher trophic level and differences in the foraging areas for mature and maturing D. gahi inferred through δ¹⁵N and δ¹³C concentrations. These differences were related to the segregation and different habitat of large mature D. gahi and suggest a food enrichment of C and N based on feeding sources other than those used by small maturing D. gahi and I. argentinus and O. ingens.     

Dihedral-angle information entropy as a gauge of secondary structure propensity

Protein structural information can be uncovered using an information-theory-based entropy and auxiliary functions by taking advantage of high-quality correlation plots between the dihedral angles around a residue and those between sequential residues. A standard information entropy for a primary sequence has been defined using the values of the probabilities of the most likely dihedral angles along the sequence. The distribution of entropy differences relative to the standard for each protein in a reference set--a sublibrary of the Protein Data Bank at the 90% sequence redundancy level--appears to be nearly Gaussian. It gives rise to an auxiliary checking function whose value signals the extent to which the dihedral angle propensities differ from typical structures. Such deviations can arise either because of incorrect dihedral angle assignments or secondary structural propensities that are atypical of the structures in the reference set. This auxiliary checking function can be readily calculated at the public website, (http://www.d2check.gatech.edu). Its utility is demonstrated here in an analysis displaying differences between experimentally and theoretically derived structures, and in the analysis of structures derived by homology modeling. A comparison of the new measure, D(2)Check, to other checking functions based on backbone conformation-namely, PROCHECK and WHAT_CHECK--is also provided.     

Energetics and structure of alanine-rich α-helices via adaptive steered molecular dynamics

The energetics and hydrogen bonding profiles of the helix-to-coil transition were found to be an additive property and to increase linearly with chain length, respectively, in alanine-rich α-helical peptides. A model system of polyalanine repeats was used to establish this hypothesis for the energetic trends and hydrogen bonding profiles. Numerical measurements of a synthesized polypeptide Ac-Y(AEAAKA)_kF-NH₂ and a natural α-helical peptide a2N (1–17) provide evidence of the hypothesis’s generality. Adaptive steered molecular dynamics was employed to investigate the mechanical unfolding of all of these alanine-rich polypeptides. We found that the helix-to-coil transition is primarily dependent on the breaking of the intramolecular backbone hydrogen bonds and independent of specific side-chain interactions and chain length. The mechanical unfolding of the α-helical peptides results in a turnover mechanism in which a 3₁₀-helical structure forms during the unfolding, remaining at a near constant population and thereby maintaining additivity in the free energy. The intermediate partially unfolded structures exhibited polyproline II helical structure as previously seen by others. In summary, we found that the average force required to pull alanine-rich α-helical peptides in between the endpoints—namely the native structure and free coil—is nearly independent of the length or the specific primary structure.     

Evaluation of stability and size distribution of sunflower oil-coated micro bubbles for localized drug delivery

Background

In recent years magnesium alloys have been intensively investigated as potential resorbable materials with appropriate mechanical and corrosion properties. Particularly in orthopedic research magnesium is interesting because of its mechanical properties close to those of natural bone, the prevention of both stress shielding and removal of the implant after surgery.

Methods

ZEK100 plates were examined in this in vitro study with Hank's Balanced Salt Solution under physiological conditions with a constant laminar flow rate. After 14, 28 and 42 days of immersion the ZEK100 plates were mechanically tested via four point bending test. The surfaces of the immersed specimens were characterized by SEM, EDX and XRD.

Results

The four point bending test displayed an increased bending strength after 6 weeks immersion compared to the 2 week group and 4 week group. The characterization of the surface revealed the presence of high amounts of O, P and Ca on the surface and small Mg content. This indicates the precipitation of calcium phosphates with low solubility on the surface of the ZEK100 plates.

Conclusions

The results of the present in vitro study indicate that ZEK100 is a potential candidate for degradable orthopedic implants. Further investigations are needed to examine the degradation behavior.     

Selection of the Internal Control Gene for Real-Time Quantitative RT-PCR Assays in Temperature Treated <Emphasis Type="Italic">Leptospira</Emphasis>

Analysis of gene expression requires sensitive, precise, and reproducible measurements for specific mRNA sequences. To avoid bias, real-time RT-PCR is referred to one or several internal control genes. Here, we sought to identify a gene to be used as normalizer by analyzing three functional distinct housekeeping genes (lipL41, flaB, and 16S rRNA) for their expression level and stability in temperature treated Leptospira cultures. Leptospira interrogans serovar Hardjo subtype Hardjoprajitno was cultured at 30°C for 7 days until a density of 10⁶ cells/ml was reached and then shifted to physiological temperatures (37°C and 42°C) and to environmental temperatures (25°C and 30°C) during a 24 h period. cDNA was amplified by quantitative PCR using SYBR Green I technology and gene-specific primers for lipL41, flaB, and 16S rRNA. Expression stability (M) was assessed by geNorm and Normfinder v.18. 16S rRNA registered an average expression stability of M = 1.1816, followed by flaB (M = 1.682) and lipL41 (M = 1.763). 16S rRNA was identified as the most stable gene and can be used as a normalizer, as it showed greater expression stability than lipL41 and flaB in the four temperature treatments. Hence, comparisons of gene expression will have a higher sensitivity and specificity.     

Contribution of Bioactive Compounds to the Antioxidant Capacity of the Edible Mushroom Neolentinus lepideus

Neolentinus lepideus is a fungus consumed by rural communities in Central America and Asia due to its rich flavor; however, little information on its chemical composition is available. With this in mind, the objective of this work was to determine the content of vitamin E and C, ergosterol, and phenolic compounds of this fungus, as well as its antioxidant capacity. The quantified bioactive compounds were two isoforms of vitamin E, highlighting α-tocopherol (3370.35 mg/100 g dry weight, DW) and ergosterol (11.70 mg/100 g DW). The total phenolic content was 164.80 mg gallic acid equivalents/100 g, and nine phenolic compounds were identified (protocatechuic, p-hydroxybenzoic, caffeic, vanillic, ferulic, salicylic, p-anisic, trans-cinnamic acids, and scopoletin). The highest antioxidant capacity was detected in the lipophilic extract with TEAC (27688 μmoles Trolox equivalents/100 g). These results suggest that lipophilic compounds are among the main bioactive compounds in N. lepideus, and they might exhibit the highest radical scavenging properties in non-polar extracts.     

Postural sway parameters using a triaxial accelerometer: comparing elderly and young healthy adults

The purpose of this study was to evaluate the sensitivity of 16 parameters derived from acceleration to detect changes caused by age and visual conditions during quiet standing and detect and minimise possible sources of unwanted variability that could affect accelerometer measures on the trunk. Twenty-seven healthy subjects, including 16 elderly (age, 69.3 ± 3.6 years) and 11 young (age, 23.6 ± 2.2 years) subjects, were evaluated. The parameters evaluated include root-mean-square values, fractal dimensions, path length, range, frequency dispersion and power spectrum among others derived from these values. These 16 parameters evaluated for each axis of movement and/or derivations resulted in 59 sub-parameters. These 59 sub-parameters were analysed in the elderly and young groups and under the open-eye and closed-eye conditions. The results showed that 30 sub-parameters detected differences for an age effect with open eyes, 18 detected differences with closed eyes, 25 detected differences for the young group standing with closed–open eyes and 37 detected differences for the elderly with closed and open eyes (p < 0.01). We used simple signal processing for the accelerometry signals to minimise the effects of unwanted variability that could affect the results. The results showed better performance compared with those results published previously using force platforms to evaluate postural sway. The results presented here should be useful for researchers who want to use accelerometry to evaluate steady postural balance.