Evaporative water loss simulation improves models’ prediction of habitat suitability for a high-elevation forest skink

Accurate evaluation of habitat availability for wildlife is relevant for ecological applications. Researchers have frequently used models to simulate habitats thermally suitable for reptiles, but these results have limited application for species highly selective for habitat humidity. Here, we use the biophysical Niche Mapper™ model to investigate impacts of vegetation cover on the habitat quality of a high-elevation forest skink, Sphenomorphus taiwanensis, and to predict changes in habitat suitability in a future warmer climate (3 °C increase in air temperature). We assess habitat suitability with different densities of canopy cover in our study areas using two ecologically relevant estimates for lizards: maximum activity time and evaporative water loss (EWL) during the activity season. We measured preferred body temperature and EWL of this species for model parameterization, and behavioral response to EWL to supplement habitat quality assessment. The results indicated that this species is sensitive to EWL and reduces its activity when dehydrated. The model predicted that denser canopy levels increase microclimate cooling and humidity, and that most canopy levels are thermally suitable for this species, as the lizard can thermoregulate to manage adverse temperatures. Nevertheless, increasing canopy density could significantly decrease EWL during activity. In the warmer climate scenario, simulated maximum activity time and EWL changed little because of thermoregulation behavior. Our results suggest that habitat preference of this species is a consequence of water and energy requirements, and we note that combining EWL and maximum activity time data can enhance model accuracy of lizards’ habitat quality in a warmer climate.     

Serum ferritin as a candidate diagnostic biomarker of polycystic ovarian syndrome: a meta-analysis

Objective: In this study, we investigated about the potential of serum ferritin as a complementary diagnostic biomarker of polycystic ovarian syndrome (PCOS) by performing a meta-analysis of existing literature.

Materials and methods: Eleven studies written in English were retrieved up to 30 June 2018. Data were extracted from the selected studies by two of the authors and was subjected to statistical analysis. Levels of serum ferritin were compared between women with PCOS and controls using the standardized mean difference (SMD) and 95% confidence interval (CI). Subgroup analysis was also performed and stratified by ethnicity (Asians versus Caucasians).

Results: Overall post-outlier outcomes indicated that elevated serum ferritin is strongly associated with PCOS (SMD: 0.52; 95% CI: 0.40–0.64; P^A?=?10^?5). Subgroup analysis by ethnicity showed no significant difference between Asian and Caucasian population. Post-outlier receiving operations characteristics curve were plotted and showed that values for serum ferritin showed good potential in discriminating patients with and without PCOS (AUC?=?0.827, p?=?0.006).

Conclusion: Our findings suggest that high serum ferritin level is significantly associated with PCOS and its potential as a biomarker is evident in its high diagnostic accuracy. However, additional studies are needed to confirm our claims.     

Evidence that phosphatidylinositol 3-kinase- and mitogen-activated protein kinase kinase-4/c-Jun NH2-terminal kinase-dependent Pathways cooperate to maintain lung cancer cell survival

Cancer cells in which the PTEN lipid phosphatase gene is deleted have constitutively activated phosphatidylinositol 3-kinase (PI3K)-dependent signaling and require activation of this pathway for survival. In non-small cell lung cancer (NSCLC) cells, PI3K-dependent signaling is typically activated through mechanisms other than PTEN gene loss. The role of PI3K in the survival of cancer cells that express wild-type PTEN has not been defined. Here we provide evidence that H1299 NSCLC cells, which express wild-type PTEN, underwent proliferative arrest following treatment with an inhibitor of all isoforms of class I PI3K catalytic activity (LY294002) or overexpression of the PTEN lipid phosphatase. In contrast, overexpression of a dominant-negative mutant of the p85alpha regulatory subunit of PI3K (Deltap85) induced apoptosis. Whereas PTEN and Delta85 both inhibited activation of AKT/protein kinase B, only Deltap85 inhibited c-Jun NH2-terminal kinase (JNK) activity. Cotransfection of the constitutively active mutant Rac-1 (Val12), an upstream activator of JNK, abrogated Deltap85-induced lung cancer cell death, whereas constitutively active mutant mitogen-activated protein kinase kinase (MKK)-1 (R4F) did not. Furthermore, LY294002 induced apoptosis of MKK4-null but not wild-type mouse embryo fibroblasts. Therefore, we propose that, in the setting of wild-type PTEN, PI3K- and MKK4/JNK-dependent pathways cooperate to maintain cell survival.     

Efficient induction of nuclear aggresomes by specific single missense mutations in the DNA-binding domain of a viral AP-1 homolog

Nuclear aggresomes induced by proteins containing an expanded polyglutamine (polyQ) tract are pathologic hallmarks of certain neurodegenerative diseases. Some GFP fusion proteins lacking a polyQ tract may also induce nuclear aggresomes in cultured cells. Here we identify single missense mutations within the basic DNA recognition region of Bam HI Z E B virus replication activator (ZEBRA), an Epstein-Barr virus (EBV)-encoded basic zipper protein without a polyQ tract, that efficiently induced the formation of nuclear aggresomes. Wild-type (WT) ZEBRA was diffusely distributed within the nucleus. Four non-DNA-binding mutants, Z(R179E), Z(R183E), Z(R190E), and Z(K178D) localized to the periphery of large intranuclear spheres, to discrete nuclear aggregates, and to the cytoplasm. Other non-DNA-binding mutants, Z(N182K), Z(N182E), and Z(S186E), did not exhibit this phenotype. The interior of the spheres contained promyelocytic leukemia and HSP70 proteins. ZEBRA mutants directly induced the nuclear aggresome pathway in cells with and without EBV. Specific cellular proteins (SC35 and HDAC6) and viral proteins (WT ZEBRA, Rta, and BMLF1) but not other cellular or viral proteins were recruited to nuclear aggresomes. Co-transfection of WT ZEBRA with aggresome-inducing mutants Z(R183E) and Z(R179E) inhibited late lytic viral protein expression and lytic viral DNA amplification. This is the first reported instance in which nuclear aggresomes are induced by single missense mutations in a viral or cellular protein. We discuss conformational changes in the mutant viral AP-1 proteins that may lead to formation of nuclear aggresomes.     

Homology inference of protein-protein interactions via conserved binding sites

The coverage and reliability of protein-protein interactions determined by high-throughput experiments still needs to be improved, especially for higher organisms, therefore the question persists, how interactions can be verified and predicted by computational approaches using available data on protein structural complexes. Recently we developed an approach called IBIS (Inferred Biomolecular Interaction Server) to predict and annotate protein-protein binding sites and interaction partners, which is based on the assumption that the structural location and sequence patterns of protein-protein binding sites are conserved between close homologs. In this study first we confirmed high accuracy of our method and found that its accuracy depends critically on the usage of all available data on structures of homologous complexes, compared to the approaches where only a non-redundant set of complexes is employed. Second we showed that there exists a trade-off between specificity and sensitivity if we employ in the prediction only evolutionarily conserved binding site clusters or clusters supported by only one observation (singletons). Finally we addressed the question of identifying the biologically relevant interactions using the homology inference approach and demonstrated that a large majority of crystal packing interactions can be correctly identified and filtered by our algorithm. At the same time, about half of biological interfaces that are not present in the protein crystallographic asymmetric unit can be reconstructed by IBIS from homologous complexes without the prior knowledge of crystal parameters of the query protein.     

Scavenger receptor class B type I localizes to a late endosomal compartment

Scavenger receptor class B type I (SR-BI) has an established role in mediating the selective uptake of cholesterol from HDL in hepatocytes, steroidogenic cells, and other tissues. SR-BI is present on the plasma membrane but also localizes to stable intracellular compartments of unknown function. Using indirect immunofluorescence and subcellular fractionation, we have investigated the subcellular distribution of SR-BI. We report that red fluorescent protein-tagged mouse SR-BI (RFP-mSR-BI) colocalizes with the late endosomal and lysosomal markers, Rab7, LBPA, and Rab9. In addition, endogenous SR-BI is also found on lysosomes and colocalizes with LAMP-2 in primary hepatocytes. Furthermore, we demonstrate that the trafficking of SR-BI through these compartments is Rab7 dependent. Interestingly, filipin staining indicates accumulation of lysosomal cholesterol in SR-BI-deficient ((-/-)) as compared with wild-type hepatocytes. In addition to its role as a plasma membrane receptor, SR-BI may function in cholesterol trafficking from late endosomes/lysosomes.     

Trivalent Iron Induced Gelation in Lambda-Carrageenan

This communication reports gelation of lambda-carrageenan, for the first time, in the presence of trivalent iron ions. Kappa-, iota- and lambda-carrageenans are sulfated polysaccharides used extensively in food, pharmaceutical and medical applications. Kappa- and iota-carrageenans show gelation in the presence of mono- and di-valent ions, but lambda-carrageenan yields only viscous solutions. Our results show that gelation in lambda-carrageenan indeed is possible, but with trivalent ions. X-ray fiber diffraction patterns of iron (III)-lambda-carrageenan are characteristic of highly oriented and polycrystalline fibers containing well resolved Bragg reflections. The elastic modulus (G′) of the product is far greater than the loss modulus (G″) indicating the thermal stability of lambda-carrageenan in the presence of iron (III) ions. This novel finding has potential to expand lambda-carrageenan's current utility beyond a viscosifying agent.     

The acute effects of a single set of contrast preloading on a loaded countermovement jump training session

The aim of this research was to assess the effect of a single set of contrast preloading on peak vertical displacement (PD) during a loaded countermovement jump (LCMJ) training session. Nine strength-trained males participated in 2 randomly assigned, crossover design testing sessions consisting of 5 sets of 6 repetitions of 20-kg LCMJs with 3-minute rest intervals between sets. The preloading intervention was performed 3 minutes after the first set and 4 minutes before the second set of 20-kg LCMJs. The control (CON) group performed 1 set of 20-kg LCMJs, whereas the jump squat (JS) group performed 1 set of 40-kg LCMJs. The number of repetitions performed during each preloading condition was varied to match total concentric work between the 2 sessions. A significant (p < 0.05) preload x set interaction for PD was observed, with the JS group jumping significantly higher during the third set performed after the preload in comparison with the CON group. Analysis of peak power output and mean power output during the concentric movement for this set revealed that as the knee flexion angle increased, the effect of the preload was augmented. These results suggest that a single set of preloading exercises enhances performance during a lower-body explosive power training session; however, the effects of a single preloading set may not peak until midway through the training session.     

Validation and Application of a Custom-Designed Targeted Next-Generation Sequencing Panel for the Diagnostic Mutational Profiling of Solid Tumors

The inevitable switch from standard molecular methods to next-generation sequencing for the molecular profiling of tumors is challenging for most diagnostic laboratories. However, fixed validation criteria for diagnostic accreditation are not in place because of the great variability in methods and aims. Here, we describe the validation of a custom panel of hotspots in 24 genes for the detection of somatic mutations in non-small cell lung carcinoma, colorectal carcinoma and malignant melanoma starting from FFPE sections, using 14, 36 and 5 cases, respectively. The targeted hotspots were selected for their present or future clinical relevance in solid tumor types. The target regions were enriched with the TruSeq approach starting from limited amounts of DNA. Cost effective sequencing of 12 pooled libraries was done using a micro flow cell on the MiSeq and subsequent data analysis with MiSeqReporter and VariantStudio. The entire workflow was diagnostically validated showing a robust performance with maximal sensitivity and specificity using as thresholds a variant allele frequency >5% and a minimal amplicon coverage of 300. We implemented this method through the analysis of 150 routine diagnostic samples and identified clinically relevant mutations in 16 genes including KRAS (32%), TP53 (32%), BRAF (12%), APC (11%), EGFR (8%) and NRAS (5%). Importantly, the highest success rate was obtained when using also the low quality DNA samples. In conclusion, we provide a workflow for the validation of targeted NGS by a custom-designed pan-solid tumor panel in a molecular diagnostic lab and demonstrate its robustness in a clinical setting.