3.9 ? structure of the nucleosome core particle determined by phase-plate cryo-EM

The Volta phase plate is a recently developed electron cryo-microscopy (cryo-EM) device that enables contrast enhancement of biological samples. Here we have evaluated the potential of combining phase-plate imaging and single particle analysis to determine the structure of a small protein–DNA complex. To test the method, we made use of a 200 kDa Nucleosome Core Particle (NCP) reconstituted with 601 DNA for which a high-resolution X-ray crystal structure is known. We find that the phase plate provides a significant contrast enhancement that permits individual NCPs and DNA to be clearly identified in amorphous ice. The refined structure from 26,060 particles has an overall resolution of 3.9 Å and the density map exhibits structural features consistent with the estimated resolution, including clear density for amino acid side chains and DNA features such as the phosphate backbone. Our results demonstrate that phase-plate cryo-EM promises to become an important method to determine novel near-atomic resolution structures of small and challenging samples, such as nucleosomes in complex with nucleosome-binding factors.     

Evaluation of different procedures for the dissociation of retinal pigmented epithelium into single viable cells

Retinal pigmented epithelium (RPE) from 7-day-old chicken embryos (stages 29 to 31) was isolated and dissociated into single cells using different procedures. The results were assessed in two ways. (1) The yield of single RPE cells per embryo was determined, and their ability to form pigmented colonies in clonal culture was tested. The most efficient and gentle procedure included isolation of the RPE in EDTA solution, trypsinization at low temperature and low enzyme concentration in the presence of EDTA, followed by incubation in culture medium for up to 4 hr. The completely dissociated cells thus obtained had a much higher plating efficiency and more uniform pattern of colony growth and differentiation than those obtained under any other conditions tested. (2) The effects of different treatments on cell junctions and morphological integrity of the cells were determined by transmission electron microscopy. EDTA solution yielded excellent separation of the epithelial sheet from the mesenchyme by dissociating it from Bruch's membrane, but had little effect on the junctions between adjacent RPE cells. Trypsinization of the epithelium under various conditions separated the basal lateral cell borders and caused loss of gap junctions, but left many cells still joined by apical tight junctions. Final disruption of the tight junctions occurred during recovery of the trypsinized cells in culture medium and was accompanied by dedifferentiation of the RPE cells.     

Distribution and migration pathways of HNK-1-immunoreactive neural crest cells in teleost fish embryos.

Whole mounts and cross-sections of embryos from three species of teleost fish were immunostained with the HNK-1 monoclonal antibody, which recognizes an epitope on migrating neural crest cells. A similar distribution and migration was found in all three species. The crest cells in the head express the HNK-1 epitope after they have segregated from the neural keel. The truncal neural crest cells begin to express the epitope while they still reside in the dorsal region of the neural keel; this has not been observed in other vertebrates. The cephalic and anterior truncal neural crest cells migrate under the ectoderm; the cephalic cells then enter into the gill arches and the anterior truncal cells into the mesentery of the digestive tract where they cease migration. These cephalic and anterior trunk pathways are similar to those described in Xenopus and chick. The neural crest cells of the trunk, after segregation, accumulate in the dorsal wedges between the somites, however, unlike in chick and rat, they do not migrate in the anterior halves of the somites but predominantly between the neural tube and the somites, the major pathway observed in carp and amphibians; some cells migrate over the somites. The HNK-1 staining of whole-mount embryos revealed a structure resembling the Rohon-Beard and extramedullary cells, the primary sensory system in amphibians. Such a system has not been described in fish.     

Isolation and partial characterization of aClostridium species transforming para-hydroxybenzoate and 3,4-dihydroxybenzoate and producing phenols as the final transformation products

Organisms present in methanogenic freshwater lake sediments from the vicinity of Athens, Georgia, were adapted to mineralize 2,4-dichlorophenol. Repeated addition of 0.5 to 2.7 mmol/liter of phenol, and later of 0.5–6.2 mmol/liter p-hydroxybenzoate (p-OHB), to such enrichments led to the conversion of p-OHB to phenol at a rate of up to 100 mmol p-OHB per liter per day. Subsequently, a spore-forming, obligately anaerobic bacterium, strain JW/Z-1, was isolated which transformed p-OHB to phenol and 3,4-dihydroxybenzoate (3,4-OHB) to catechol (1,2-dihydroxybenzene) stoichiometrically without further metabolism of the phenols. The strain did not transform benzoate, 4-chlorophenol, 2,4-dichlorophenol, 4-chlorobenzoate, o- and m-hydroxybenzoate, 2,4- and 3,5-dihydroxybenzoate, 2,3,4- and 3,4,5-trihydroxybenzoate, or 4-aminobenzoate. Yeast extract was required for growth of strain JW/Z-1 and only high concentrations of casein hydrolysate or tryptone could substitute it, to some extent. Except for sodium acetate, and some amino acids together with a 20-fold increased concentration of vitamins, no single carbohydrate or defined organic compound has been found to support growth of this strain in the presence (or in the absence) of 0.2 to 0.5% (w/v) yeast extract. The fermentation products during growth on yeast extract indicated that the metabolism of amino acid degradation was the major source for growth. The decarboxylating activity was inducible by p-OHB for the decarboxylation of p-OHB, and at a lower rate for 3,4-OHB, and by 3,4-OHB only for 3,4-OHB, suggesting that two different enzyme systems exist. The addition of the aromatic amino acids phenol or benzoate did not induce the decarboxylation activity in cultures growing with yeast extract. Growth was observed at temperatures ranging from 12–41°C (T_opt, 33–34°C) and at pH-values ranging from 6.0–10.0 (pH_opt, 7.2–8.2). The shortest doubling time observed for strain JW/Z-1 was 3.2 hours.     

A simple method to estimate the probable distribution of species

Species distribution models (SDMs) are broadly used to predict species distributions from available presence data. However, SDMs results have been criticized for several reasons mainly related to two basic characteristics of most SDMs: 1) general lack of reliable species absence information, 2) the frequent use of an arbitrary geographical extent (GE) or accessible area of the species. These impediments have motivated us to generate a procedure called niche of occurrence (NOO). NOO provides the probable distribution of species (realized niche) relying solely on partial information about presence of species. It operates within a natural geographical extent delimited by available observations and avoids using misleading thresholds to obtain binary presence–absence estimations when the species prevalence is unknown. In this study the main characteristics of NOO are presented, comparing its performance with other recognized and more complex SDMs by using virtual species to avoid the omnipresent error sources of real data sets.     

High visceral fat mass and high liver fat are associated with resistance to lifestyle intervention

Objective: High visceral adipose tissue (VAT) and high liver fat (LF) are associated with the metabolic syndrome and diabetes. We studied changes in these two fat depots during weight loss and analyzed whether VAT and LF at baseline predict the response to lifestyle intervention. Research Methods and Procedures: One hundred twelve subjects (48 men and 64 women; age, 46 ± 11 years; BMI, 29.2 ± 4.4 kg/m²) were studied after a follow up‐time of 264 ± 60 (SD) days. Insulin sensitivity was estimated from the oral glucose tolerance test. Body fat depots were quantified using magnetic resonance imaging and spectroscopy. Results: Cross‐sectionally high VAT (r = ?0.22, p = 0.02) and high LF (r = ?0.36, p < 0.0001) were independently associated with low insulin sensitivity. With intervention, BMI (?3.0%), VAT (?12.0%), and LF (?33.0%) were reduced (all p < 0.001). Insulin sensitivity was improved (+17%, p < 0.01). The changes in BMI (r = ?0.41), VAT (r = ?0.28), and LF (r = ?0.39) were associated with the increase in insulin sensitivity (all p < 0.01). High VAT (r = ?0.28, p = 0.01) and high LF (r = ?0.38, p < 0.01) at baseline were associated with a lesser increase in insulin sensitivity. Discussion: Baseline values and changes in BMI, VAT, and LF are related to changes in insulin sensitivity during lifestyle intervention. Subjects with high VAT and LF have a lower chance of profiting from lifestyle intervention and may require intensified lifestyle prevention strategies or even pharmacological approaches to improve insulin sensitivity.     

Individual assessment of arteriosclerosis by empiric clinical profiling

Background

Arteriosclerosis is a common cause of chronic morbidity and mortality. Myocardial infarction, stroke or other cardiovascular events identify vulnerable patients who suffer from symptomatic arteriosclerosis. Biomarkers to identify vulnerable patients before cardiovascular events occur are warranted to improve care for affected individuals. We tested how accurately basic clinical data can describe and assess the activity of arteriosclerosis in the individual patient.

Methodology/Principal Findings

269 in-patients who were treated for various conditions at the department of general medicine of an academic tertiary care center were included in a cross-sectional study. Personal history and clinical examination were obtained. When paraclinical tests were performed, the results were added to the dataset. The numerical variables in the clinical examination were statistically compared between patients with proven symptomatic arteriosclerosis (n = 100) and patients who had never experienced cardiovascular events in the past (n = 110). 25 variables were different between these two patient groups and contributed to the disease activity score. The percentile distribution of these variables defined the empiric clinical profile. Anthropometric data, signs of arterial, cardiac and renal disease, systemic inflammation and health economics formed the major categories of the empiric clinical profile that described an individual patient''s disease activity. The area under the curve of the receiver operating curve for symptomatic arteriosclerosis was 0.891 (95% CI 0.799-0.983) for the novel disease activity score compared to 0.684 (95% CI 0.600-0.769) for the 10-year risk calculated according to the Framingham score. In patients suffering from symptomatic arteriosclerosis, the disease activity score deteriorated more rapidly after two years of follow-up (from 1.25 to 1.48, P = 0.005) compared to age- and sex-matched individuals free of cardiovascular events (from 1.09 to 1.19, P = 0.125).

Conclusions/Significance

Empiric clinical profiling and the disease activity score that are based on accessible, available and affordable clinical data are valid markers for symptomatic arteriosclerosis.     

An additional human chromosome 21 causes suppression of neural fate of pluripotent mouse embryonic stem cells in a teratoma model

Background

Down syndrome (DS), caused by trisomy of human chromosome 21 (HSA21), is the most common genetic cause of mental retardation in humans. Among complex phenotypes, it displays a number of neural pathologies including smaller brain size, reduced numbers of neurons, reduced dendritic spine density and plasticity, and early Alzheimer-like neurodegeneration. Mouse models for DS show behavioural and cognitive defects, synaptic plasticity defects, and reduced hippocampal and cerebellar neuron numbers. Early postnatal development of both human and mouse-model DS shows the reduced capability of neuronal precursor cells to generate neurons. The exact molecular cause of this reduction, and the role played by increased dosage of individual HSA21 genes, remain unknown.

Results

We have subcutaneously injected mouse pluripotent ES cells containing a single freely segregating supernumerary human chromosome 21 (HSA21) into syngeneic mice, to generate transchromosomic teratomas. Transchromosomic cells and parental control cells were injected into opposite flanks of thirty mice in three independent experiments. Tumours were grown for 30 days, a time-span equivalent to combined intra-uterine, and early post-natal mouse development. When paired teratomas from the same animals were compared, transchromosomic tumours showed a three-fold lower percentage of neuroectodermal tissue, as well as significantly reduced mRNA levels for neuron specific (Tubb3) and glia specific (Gfap) genes, relative to euploid controls. Two thirds of transchromosomic tumours also showed a lack of PCR amplification with multiple primers specific for HSA21, which were present in the ES cells at the point of injection, thus restricting a commonly retained trisomy to less than a third of HSA21 genes.

Conclusion

We demonstrate that a supernumerary chromosome 21 causes Inhibition of Neuroectodermal DIfferentiation (INDI) of pluripotent ES cells. The data suggest that trisomy of less than a third of HSA21 genes, in two chromosomal regions, might be sufficient to cause this effect.     

A multivalent approach to the discovery of long-acting β(2)-adrenoceptor agonists for the treatment of asthma and COPD

A multivalent approach was applied to the design of long-acting inhaled β(2)-adrenoceptor agonists. A series of dimeric arylethanolamines based on the short acting β(2)-adrenoceptor agonist albuterol were prepared, varying the nature and length of the linker between the basic nitrogens. None of the C(2)-symmetric dimers demonstrated increased potency, however dimer 5j, derived from 4-phenethylamine, was found to have increased binding potency in vitro relative to the parent monomer. Optimization of this structure led to the identification of 22 (milveterol) which demonstrates high potency in vitro and long duration of action in a guinea pig model of bronchoprotection.