Beyond small molecules: targeting G-quadruplex structures with oligonucleotides and their analogues

G-Quadruplexes (G4s) are widely studied secondary DNA/RNA structures, naturally occurring when G-rich sequences are present. The strategic localization of G4s in genome areas of crucial importance, such as proto-oncogenes and telomeres, entails fundamental implications in terms of gene expression regulation and other important biological processes. Although thousands of small molecules capable to induce G4 stabilization have been reported over the past 20 years, approaches based on the hybridization of a synthetic probe, allowing sequence-specific G4-recognition and targeting are still rather limited. In this review, after introducing important general notions about G4s, we aim to list, explain and critically analyse in more detail the principal approaches available to target G4s by using oligonucleotides and synthetic analogues such as Locked Nucleic Acids (LNAs) and Peptide Nucleic Acids (PNAs), reporting on the most relevant examples described in literature to date.     

Characterization of complex III deficiency and liver dysfunction in GRACILE syndrome caused by a BCS1L mutation

A homozygous mutation in the complex III chaperone BCS1L causes GRACILE syndrome (intrauterine growth restriction, aminoaciduria, cholestasis, hepatic iron overload, lactacidosis). In control and patient fibroblasts we localized BCS1L in inner mitochondrial membranes. In patient liver, kidney, and heart BCS1L and Rieske protein levels, as well as the amount and activity of complex III, were decreased. Major histopathology was found in kidney and liver with cirrhosis and iron deposition, but of iron-related proteins only ferritin levels were high. In placenta from a GRACILE fetus, the ferrooxidases ceruloplasmin and hephaestin were upregulated suggesting association between iron overload and placental dysfunction.     

Recommendations for the use of bioresorbable vascular scaffolds in percutaneous coronary interventions

Background

To eliminate some of the potential late limitations of permanent metallic stents, the bioresorbable coronary stents or ‘bioresorbable vascular scaffolds’ (BVS) have been developed.

Methods

We reviewed all currently available clinical data on BVS implantation.

Results

Since the 2015 position statement on the appropriateness of BVS in percutaneous coronary interventions, several large randomised trials have been presented. These have demonstrated that achieving adequate 1 and 2 year outcomes with these first-generation BVS is not straightforward. These first adequately powered studies in non-complex lesions showed worse results if standard implantation techniques were used for these relatively thick scaffolds. Post-hoc analyses hypothesise that outcomes similar to current drug-eluting stents are still possible if aggressive lesion preparation, adequate sizing and high-pressure postdilatation are implemented rigorously. As long as this has not been confirmed in prospective studies the usage should be restricted to experienced centres with continuous outcome monitoring. For more complex lesions, results are even more disappointing and usage should be discouraged. When developed, newer generation scaffolds with thinner struts or faster resorption rates are expected to improve outcomes. In the meantime prolonged dual antiplatelet therapy (DAPT, beyond one year) is recommended in an individualised approach for patients treated with current generation BVS.

Conclusion

The new 2017 recommendations downgrade and limit the use of the current BVS to experienced centres within dedicated registries using the updated implantation protocol and advise the prolonged usage of DAPT. In line with these recommendations the manufacturer does not supply devices to the hospitals without such registries in place.

     

Ontogeny of the jaws of monogonont rotifers: the malleate trophi of Rhinoglena and Proalides (Ploima,Epiphanidae)

Information on the embryonic development of the malleate trophi in Epiphanidae (Rotifera, Monogononta, Ploima) is presented, based on scanning electron microscopy observations in Rhinoglena fertoeensis, R. frontalis, R. kutikovae, R. tokioensis, and Proalides tentaculatus, to contribute to the understanding of this structure of high evolutionary and functional relevance in Rotifera. The first observable and distinctly sclerotized structures were a double row of median transversal sclerites along the longitudinal axis, wherein the future unci, rostellar scleropili, cristae rami, and basal apophyses became recognizable. Fulcrum and manubria arose subsequently; the fulcrum sclerites were longitudinally ordered in a double layer. The rami chambers developed last as lamellar structures. Unci appeared as separate thin, elongate elements, the primary uncini, developing to uncus plates by transversal growth and apposition of sclerite material on the shafts of the uncini. The heads of the uncini showed their greatest development after fusion of their shafts into uncus plates. The interjacent spaces between the heads functioned as a mold, organizing bundles of sclerites which developed into the uniseriate, zigzag‐shaped cristae rami. The fulcrum attained its definite shape by elongation of the double layer of rod‐shaped sclerites into appressed sclerofibrillae. Manubria became visible as a proximal ridge of sclerites, whereupon a triangular lamella composed of crisscross‐oriented sclerites developed distally, growing out to the manubrial chambers. Ramus chambers originated from two longitudinal amorphous lamellae incorporating the median rami sclerites and closing from distal to proximal; subbasal chambers were formed before the basal chambers.     

Modulation of inositol 1,4,5-trisphosphate binding to the recombinant ligand-binding site of the type-1 inositol 1,4, 5-trisphosphate receptor by Ca2+ and calmodulin

A recombinant protein (Lbs-1) containing the N-terminal 581 amino acids of the mouse type 1 inositol 1,4,5-trisphosphate receptor (IP3R-1), including the complete IP3-binding site, was expressed in the soluble fraction of E. coli. The characteristics of IP3 binding to this protein were similar as observed previously for the intact IP3R-1. Ca2+ dose-dependently inhibited IP3 binding to Lbs-1 with an IC50 of about 200 nM. This effect represented a decrease in the affinity of Lbs-1 for IP3, because the Kd increased from 115 +/- 15 nM in the absence to 196 +/- 18 nM in the presence of 5 microM Ca2+. The maximal effect of Ca2+ on Lbs-1 (5 microM Ca2+, 42.0 +/- 6.4% inhibition) was similar to the maximal inhibition observed for microsomes of insect Sf9 cells expressing full-length IP3R-1 (33.8 +/- 10.2%). Conceivably, the two contiguous Ca2+-binding sites (residues 304-450 of mouse IP3R-1) previously found by us (Sienaert, I., Missiaen, L., De Smedt, H., Parys, J.B., Sipma, H., and Casteels, R. (1997) J. Biol. Chem. 272, 25899-25906) mediate the effect of Ca2+ on IP3 binding to IP3R-1. Calmodulin also dose-dependently inhibited IP3 binding to Lbs-1 with an IC50 of about 3 microM. Maximal inhibition (10 microM calmodulin, 43.1 +/- 5.9%) was similar as observed for Sf9-IP3R-1 microsomes (35.8 +/- 8.7%). Inhibition by calmodulin occurred independently of Ca2+ and was additive to the inhibitory effect of 5 microM Ca2+ (together 74.5 +/- 5.1%). These results suggest that the N-terminal ligand-binding region of IP3R-1 contains a calmodulin-binding domain that binds calmodulin independently of Ca2+ and that mediates the inhibition of IP3 binding to IP3R-1.     

Biomarker discovery using a comparative omics approach in a mouse model developing heterogeneous mammary cancer subtypes

Identification of biomarkers for early breast cancer detection in blood is a challenging task, since breast cancer is a heterogeneous disease with a wide range of tumor subtypes. This is envisioned to result in differences in serum protein levels. The p53(R270H/+) WAPCre mouse model is unique in that these mice spontaneously develop both ER- and ER+ tumors, in proportions comparable to humans. Therefore, these mice provide a well-suited model system to identify human relevant biomarkers for early breast cancer detection that are additionally specific for different tumor subtypes. Mammary gland tumors were obtained from p53(R270H/+) WAPCre mice and cellular origin, ER, and HER2 status were characterized. We compared gene expression profiles for tumors with different characteristics versus control tissue, and determined genes differentially expressed across tumor subtypes. By using literature data (Gene Ontology, UniProt, and Human Plasma Proteome), we further identified protein candidate biomarkers for blood-based detection of breast cancer. Functional overrepresentation analysis (using Gene Ontology, MSigDB, BioGPS, Cancer GeneSigDB, and proteomics literature data) showed enrichment for several processes relevant for human breast cancer. Finally, Human Protein Atlas data were used to obtain a prioritized list of 16 potential biomarkers that should facilitate further studies on blood-based breast cancer detection in humans.     

Biodiversity,biogeography, and connectivity of polychaetes in the world's largest marine minerals exploration frontier

Aim

The abyssal Clarion-Clipperton Zone (CCZ), Pacific Ocean, is an area of commercial importance owing to the growing interest in mining high-grade polymetallic nodules at the seafloor for battery metals. Research into the spatial patterns of faunal diversity, composition, and population connectivity is needed to better understand the ecological impacts of potential resource extraction. Here, a DNA taxonomy approach is used to investigate regional-scale patterns of taxonomic and phylogenetic alpha and beta diversity, and genetic connectivity, of the dominant macrofaunal group (annelids) across a 6 million km² region of the abyssal seafloor.

Location

The abyssal seafloor (3932–5055 m depth) of the Clarion-Clipperton Zone, equatorial Pacific Ocean.

Methods

We used a combination of new and published barcode data to study 1866 polychaete specimens using molecular species delimitation. Both phylogenetic and taxonomic alpha and beta diversity metrics were used to analyse spatial patterns of biodiversity. Connectivity analyses were based on haplotype distributions for a subset of the studied taxa.

Results

DNA taxonomy identified 291–314 polychaete species from the COI and 16S datasets respectively. Taxonomic and phylogenetic beta diversity between sites were relatively high and mostly explained by lineage turnover. Over half of pairwise comparisons were more phylogenetically distinct than expected based on their taxonomic diversity. Connectivity analyses in abundant, broadly distributed taxa suggest an absence of genetic structuring driven by geographical location.

Main Conclusions

Species diversity in abyssal Pacific polychaetes is high relative to other deep-sea regions. Results suggest that environmental filtering, where the environment selects against certain species, may play a significant role in regulating spatial patterns of biodiversity in the CCZ. A core group of widespread species have diverse haplotypes but are well connected over broad distances. Our data suggest that the high environmental and faunal heterogeneity of the CCZ should be considered in future policy decisions.     

The total protein content in the blood serum of vertebrates

The total protein content in the blood serum of 416 species and subspecies of vertebrates is determined by the microbiuret method. Generally speaking the total protein content of the serum shows an increase with a higher evolutionary level. The difference between the mammals and the other groups is particularly large. This increase is probably attributable to a number of factors, for instance adaptation to living on land, development of the circulatory system, the development of adaptive immunity and the forming of specific transport proteins. A connection between albumin content and level of development can also be noticed.