A comparative study of ex vivo skin optical clearing using two‐photon microscopy

Multiphoton tomography (MPT) is a prospective tool for imaging the skin structure. Aiming to increase the probing depth, a comparative ex vivo study of optical clearing of porcine ear skin was performed by using two optical clearing agents (OCAs), i.e., glycerol and iohexol (Omnipaque^TM) at different concentrations, which exhibit different osmotic properties. The results show that a topical application of glycerol or Omnipaque^TM solutions onto the skin for 60 min significantly improved the depth and contrast of the MPT signals. By utilizing 40%, 60% and 100% glycerol, and 60% and 100% Omnipaque^TM it was demonstrated that both agents improve autofluorescence and SHG (second harmonic generation) signals from the skin. At the applied concentrations and agent time exposure, glycerol is more effective than Omnipaque^TM. However, tissue shrinkage and cell morphology changes were found for highly concentrated glycerol solutions. Omnipaque^TM, on the contrary, increases the safety and has no or minimal tissue shrinkage during the optical clearing process. Moreover Omnipaque^TM allows for robust multimodal optical/X‐ray imaging with automatically matched optically cleared and X‐ray contrasted tissue volumes. These findings make Omnipaque^TM more prospective than glycerol for some particular application.

     

Evolution of evolvability in gene regulatory networks

Gene regulatory networks are perhaps the most important organizational level in the cell where signals from the cell state and the outside environment are integrated in terms of activation and inhibition of genes. For the last decade, the study of such networks has been fueled by large-scale experiments and renewed attention from the theoretical field. Different models have been proposed to, for instance, investigate expression dynamics, explain the network topology we observe in bacteria and yeast, and for the analysis of evolvability and robustness of such networks. Yet how these gene regulatory networks evolve and become evolvable remains an open question.     

Clonal crayfish as biological model: a review on marbled crayfish

Since the mid-twentieth century, numerous vertebrates and invertebrates have been used as model organisms and become indispensable tools for exploring a broad range of biological and ecological processes. Crayfish seem to be adequate models which resulted in their involvement in research. In the two decades since its discovery, ongoing research has confirmed that the marbled crayfish (Procambarus virginalis Lyko, 2017) is an ideal taxon in this regard, especially due to its almost continuous asexual reproduction providing a source of genetically identical offspring. This review provides an overview of the occurrence, biology, ecology, ethology, and human exploitation of marbled crayfish with primary focus on its use as a laboratory model organism as well as potential risks to native biota in case of its introduction. Genetic uniformity, ease of culture, and a broad behaviour repertoire fosters the use of marbled crayfish in epigenetics and developmental biology, as well as physiological, ecotoxicological, and ethological research. Marbled crayfish could be further exploited for basic and applied fields of science such as evolutionary biology and clonal tumour evolution. However, due to its high invasive potential in freshwater environments security measures must be taken to prevent its escape into the wild.     

DCC Expression by Neurons Regulates Synaptic Plasticity in the Adult Brain

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Highlights? DCC and netrin-1 are enriched at synapses in the adult mouse forebrain ? DCC is enriched in the PSD and regulates dendritic spine morphology ? LTP induction and memory formation require DCC expression by neurons ? DCC activation of Src is required for NMDAR-dependent LTP in adult CNS     

144 Sculpting light with DNA origami

We used the DNA origami method (Rothemund, 2006) for the fabrication of self-assembled nanoscopic materials (Seeman, 2010). In DNA origami, a virus-based 8?kilobase-long DNA single-strand is folded into shape with the help of ～ 200 synthetic oligonucleotides. The resulting DNA nanostructures can be designed to adopt any three-dimensional shape and can be addressed through DNA hybridization or chemical modification with nanometer precision. We have realized that complex assemblies of nanoparticles, including magnetic, fluorescent, and plasmonic nanoparticles. Such nanoconstructs may exhibit striking optical properties such as strong optical activity in the visible range (Kuzyk et al., 2012). To this end, plasmonic particles were assembled in solution to form helices of controlled handedness. We achieved spatial control over particle placement better than 2?nm and attachment yields of 97% and above. As a collective optical response emerging from our dispersed nanostructures, we detected pronounced circular dichroism (CD) originating from the plasmon–plasmon interactions in the particle helices. In recent experiments, we were able to show that the optical response of chiral biomolecules can be transferred from the UV into the visible region in plasmonic hotspots. Thus, sensitive detection of chiral biomolecules may become feasible in the near future. We also found that the orientation of the helices in respect to the incoming light beam critically influences the resulting CD spectra. Our results can be explained with theoretical models based on plasmonic dipole interaction and demonstrate the potential of DNA origami for the assembly of metafluids with designed optical properties.     

Human-specific subfamilies of HERV-K (HML-2) long terminal repeats: three master genes were active simultaneously during branching of hominoid lineages

Using 40 known human-specific LTR sequences, we have derived a consensus sequence for an evolutionary young HERV-K (HML-2) LTR family, which was named the HS family. In the human genome the HS family is represented by approximately 150-160 LTR sequences, 90% of them being human-specific (hs). The family can be subdivided into two subfamilies differing in five linked nucleotide substitutions: HS-a and HS-b of 5.8 and 10.3 Myr evolutionary ages, respectively. The HS-b subfamily members were transpositionally active both before the divergence of the human and chimpanzee ancestor lineages and after it in both lineages. The HS-a subfamily comprises only hs LTRs. These and other data strongly suggest that at least three "master genes" of HERV-K (HML-2) LTRs were active in the human ancestor lineage after the human-chimpanzee divergence. We also found hs HERV-K (HML-2) LTRs integrations in introns of 12 human genes and identified 13 new hs HERV-K (HML-2) LTRs.     

Reduced Glomerular Filtration Rate and Its Association with Clinical Outcome in Older Patients at Risk of Vascular Events: Secondary Analysis

Background

Reduced glomerular filtration rate (GFR) is associated with increased cardiovascular risk in young and middle aged individuals. Associations with cardiovascular disease and mortality in older people are less clearly established. We aimed to determine the predictive value of the GFR for mortality and morbidity using data from the 5,804 participants randomized in the Prospective Study of Pravastatin in the Elderly at Risk (PROSPER).

Methods and Findings

Glomerular filtration rate was estimated (eGFR) using the Modification of Diet in Renal Disease equation and was categorized in the ranges ([20–40], [40–50], [50–60]) ≥ 60 ml/min/1.73 m². Baseline risk factors were analysed by category of eGFR, with and without adjustment for other risk factors. The associations between baseline eGFR and morbidity and mortality outcomes, accrued after an average of 3.2 y, were investigated using Cox proportional hazard models adjusting for traditional risk factors. We tested for evidence of an interaction between the benefit of statin treatment and baseline eGFR status. Age, low-density lipoprotein (LDL) and high-density lipoprotein (HDL) cholesterol, C-reactive protein (CRP), body mass index, fasting glucose, female sex, histories of hypertension and vascular disease were associated with eGFR (p = 0.001 or less) after adjustment for other risk factors. Low eGFR was independently associated with risk of all cause mortality, vascular mortality, and other noncancer mortality and with fatal and nonfatal coronary and heart failure events (hazard ratios adjusted for CRP and other risk factors (95% confidence intervals [CIs]) for eGFR < 40 ml/min/1.73m² relative to eGFR ≥ 60 ml/min/1.73m² respectively 2.04 (1.48–2.80), 2.37 (1.53–3.67), 3.52 (1.78–6.96), 1.64 (1.18–2.27), 3.31 (2.03–5.41). There were no nominally statistically significant interactions (p < 0.05) between randomized treatment allocation and eGFR for clinical outcomes, with the exception of the outcome of coronary heart disease death or nonfatal myocardial infarction (p = 0.021), with the interaction suggesting increased benefit of statin treatment in subjects with impaired GFRs.

Conclusions

We have established that, in an elderly population over the age of 70 y, impaired GFR is associated with female sex, with presence of vascular disease, and with levels of other risk factors that would be associated with increased risk of vascular disease. Further, impaired GFR is independently associated with significant levels of increased risk of all cause mortality and fatal vascular events and with composite fatal and nonfatal coronary and heart failure outcomes. Our analyses of the benefits of statin treatment in relation to baseline GFR suggest that there is no reason to exclude elderly patients with impaired renal function from treatment with a statin.     

Citric acid production in chemically defined media by Aspergillus niger

Summary The effect of changing the composition of a chemically defined medium on citric acid production by Aspergillus niger was investigated. High and reproducible amounts of citric acid were obtained with deionized commercial sugar solutions, proper phosphate concentrations, low initial pH values and suitable amounts of copper as growth inhibiting agent.Comparison of high and low yielding process parameters showed that under high yielding conditions, (deionized sugar, Cu⁺⁺ addition) besides more citric acid, less mycelium and less mycelial lipids were formed; the consumption of sugar, nitrogen and phosphorus was related to the amount of biomass.Partly presented at the XII. International Congress of Microbiology; München, September 3–8, 1978     

Mapping functional associations in the entire genome of Drosophila melanogaster using fusion analysis

We have previously shown that the detection of gene fusion events can contribute towards the elucidation of functional associations of proteins within entire genomes. Here we have analysed the entire genome of Drosophila melanogaster using fusion analysis and two additional constraints that improve the reliability of the predictions, viz. low sequence similarity and low degree of paralogy of the component proteins involved in a fusion event. Imposing these constraints, the total number of unique component pairs is reduced from 18 654 to a mere 220 cases, which are expected to represent some of the most reliably detected functionally associated proteins. Using additional information from sequence databases, we have been able to detect pairs of functionally associated proteins with important functions in cellular and developmental pathways, such as spermatogenesis and programmed cell death.     

An evolutionary intra-molecular shift in the preferred U3 snoRNA binding site on pre-ribosomal RNA

Correct docking of U3 small nucleolar RNA (snoRNA) on pre-ribosomal RNA (pre-rRNA) is essential for rRNA processing to produce 18S rRNA. In this report, we have used Xenopus oocytes to characterize the structural requirements of the U3 snoRNA 3′-hinge interaction with region E1 of the external transcribed spacer (ETS) of pre-rRNA. This interaction is crucial for docking to initiate rRNA processing. 18S rRNA production was inhibited when fewer than 6 of the 8 bp of the U3 3′–hinge complex with the ETS could form; moreover, base pairing involving the right side of the 3′-hinge was more important than the left. Increasing the length of the U3 hinge–ETS interaction by 9 bp impaired rRNA processing. Formation of 18S rRNA was also inhibited by swapping the U3 5′- and 3′-hinge interactions with the ETS or by shifting the base pairing of the U3 3′-hinge to the sequence directly adjacent to ETS region E1. However, 18S rRNA production was partially restored by a compensatory shift that allowed the sequence adjacent to the U3 3′-hinge to pair with the eight bases directly adjacent to ETS region E1. The results suggest that the geometry of the U3 snoRNA interaction with the ETS is critical for rRNA processing.