Liver-type fatty acid binding protein interacts with hepatocyte nuclear factor 4α

Hepatocyte nuclear factor 4α (HNF4α) regulates liver type fatty acid binding protein (L-FABP) gene expression. Conversely as shown herein, L-FABP structurally and functionally also interacts with HNF4α. Fluorescence resonance energy transfer (FRET) between Cy3-HNF4α (donor) and Cy5-L-FABP (acceptor) as well as FRET microscopy detected L-FABP in close proximity (∼80 Å) to HNF4α, binding with high affinity K_d ∼250–300 nM. Circular dichroism (CD) determined that the HNF4α/L-FABP interaction altered protein secondary structure. Finally, L-FABP potentiated transactivation of HNF4α in COS7 cells. Taken together, these data suggest that L-FABP provides a signaling path to HNF4α activation in the nucleus.     

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain <1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062–147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217–73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.     

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

Drug repositioning applies established drugs to new disease indications with increasing success. A pre-requisite for drug repurposing is drug promiscuity (polypharmacology) – a drug’s ability to bind to several targets. There is a long standing debate on the reasons for drug promiscuity. Based on large compound screens, hydrophobicity and molecular weight have been suggested as key reasons. However, the results are sometimes contradictory and leave space for further analysis. Protein structures offer a structural dimension to explain promiscuity: Can a drug bind multiple targets because the drug is flexible or because the targets are structurally similar or even share similar binding sites? We present a systematic study of drug promiscuity based on structural data of PDB target proteins with a set of 164 promiscuous drugs. We show that there is no correlation between the degree of promiscuity and ligand properties such as hydrophobicity or molecular weight but a weak correlation to conformational flexibility. However, we do find a correlation between promiscuity and structural similarity as well as binding site similarity of protein targets. In particular, 71% of the drugs have at least two targets with similar binding sites. In order to overcome issues in detection of remotely similar binding sites, we employed a score for binding site similarity: LigandRMSD measures the similarity of the aligned ligands and uncovers remote local similarities in proteins. It can be applied to arbitrary structural binding site alignments. Three representative examples, namely the anti-cancer drug methotrexate, the natural product quercetin and the anti-diabetic drug acarbose are discussed in detail. Our findings suggest that global structural and binding site similarity play a more important role to explain the observed drug promiscuity in the PDB than physicochemical drug properties like hydrophobicity or molecular weight. Additionally, we find ligand flexibility to have a minor influence.     

Chemerin Is an Antimicrobial Agent in Human Epidermis

Chemerin, a chemoattractant ligand for chemokine-like receptor 1 (CMKLR1) is predicted to share similar tertiary structure with antibacterial cathelicidins. Recombinant chemerin has antimicrobial activity. Here we show that endogenous chemerin is abundant in human epidermis, and that inhibition of bacteria growth by exudates from organ cultures of primary human skin keratinocytes is largely chemerin-dependent. Using a panel of overlapping chemerin-derived synthetic peptides, we demonstrate that the antibacterial activity of chemerin is primarily mediated by Val⁶⁶-Pro⁸⁵, which causes direct bacterial lysis. Therefore, chemerin is an antimicrobial agent in human skin.     

Cardiometabolic risks during anabolic hormone supplementation in older men

Objective:

To determine the cardiometabolic risks of testosterone and growth hormone (GH) replacement therapy to youthful levels during aging.

Design and Methods:

A double‐masked, partially placebo controlled study in 112 men 65‐90 years‐old was conducted. Transdermal testosterone (5 g vs. 10 g/day) using a Leydig Cell Clamp and subcutaneous recombinant GH (rhGH) (0 vs. 3 vs. 5 μg/kg/day) were administered for 16‐weeks. Measurements included testosterone and IGF‐1 levels, body composition by DEXA, and cardiometabolic risk factors (upper body fat, blood pressure, insulin sensitivity, fasting triglycerides, HDL‐cholesterol, and serum adiponectin) at baseline and after 16 weeks of treatment.

Results:

Some cardiometabolic factors improved (total and trunk fat, triglycerides, HDL‐cholesterol) and others worsened (systolic blood pressure, insulin sensitivity index [QUICKI], adiponectin). Cardiometabolic risk composite scores (CRCSs) improved (?0.69 ± 1.55, P < 0.001). In multivariate analyses, QUICKI, triglycerides, and HDL‐cholesterol contributed 33%, 16%, and 14% of the variance in CRCS, respectively. Pathway analyses indicated that changes in fat and lean mass were related to individual cardiometabolic variables and CRCS in a complex manner. Changes in BMI, reflecting composite effects of changes in fat and lean mass, were more robustly associated with cardiometabolic risks than changes in fat mass or LBM individually.

Conclusions:

Testosterone and rhGH administration was associated with diverse changes in individual cardiometabolic risk factors, but in aggregate appeared not to worsen cardiometabolic risk in healthy older men after 4‐months. The long‐term effects of these and similar anabolic therapies on cardiovascular events should be investigated in populations with greater functional limitations along with important health disabilities including upper body obesity and other cardiometabolic risks.

     

Real‐Time Investigation of Intercalation and Structure Evolution in Printed Polymer:Fullerene Bulk Heterojunction Thin Films

The complex intermixing morphology is critical for the performance of the nanostructured polymer:fullerene bulk heterojunction (BHJ) solar cells. Here, time resolved in situ grazing incidence X‐ray diffraction and grazing incidence small angle X‐ray scattering are used to track the structure formation of BHJ thin films formed from the donor polymer poly(2,5‐bis(3‐hexadecylthiophen‐2‐yl)thieno[3,2‐b]thiophene) with different fullerene derivative acceptors. The formation of stable bimolecular crystals through the intercalation of fullerene molecules between the side chains of polymer crystallites is investigated. Such systems exhibit more efficient exciton dissociation but lower photo‐conductance and faster decay of charges. On the basis of the experimental observations, intercalation obviously takes place before or with the formation of the crystalline polymer domains. It results in more stable structures whose volume remains constant upon further drying. Three distinct periods of drying are observed and the formation of unidimensional fullerene channels along the π‐stacking direction of polymer crystallites is confirmed.     

Comparison of the Morphology Development of Polymer–Fullerene and Polymer–Polymer Solar Cells during Solution‐Shearing Blade Coating

In this work, the detailed morphology studies of polymer poly(3‐hexylthiophene‐2,5‐diyl) (P3HT):fullerene(PCBM) and polymer(P3HT):polymer naphthalene diimide thiophene (PNDIT) solar cell are presented to understand the challenge for getting high performance all‐polymer solar cells. The in situ X‐ray scattering and optical interferometry and ex situ hard and soft X‐ray scattering and imaging techniques are used to characterize the bulk heterojunction (BHJ) ink during drying and in dried state. The crystallization of P3HT polymers in P3HT:PCBM bulk heterojunction shows very different behavior compared to that of P3HT:PNDIT BHJ due to different mobilities of P3HT in the donor:acceptor glass. Supplemented by the ex situ grazing incidence X‐ray diffraction and soft X‐ray scattering, PNDIT has a lower tendency to form a mixed phase with P3HT than PCBM, which may be the key to inhibit the donor polymer crystallization process, thus creating preferred small phase separation between the donor and acceptor polymer.