Is the prion domain of soluble Ure2p unstructured?

The [URE3] prion is a self-propagating amyloid form of the Ure2 protein of Saccharomyces cerevisiae. Deletions in the C-terminal nitrogen regulation domain of Ure2p increase the frequency with which the N-terminal prion domain polymerizes into the prion form, suggesting that the C-terminus stabilizes the prion domain or that the structured C-terminal region sterically impairs amyloid formation. We find by in vivo two-hybrid analysis no evidence of interaction of prion domain and C-terminal domain. Furthermore, surface plasmon resonance spectrometry shows no evidence of interaction of prion domain and C-terminal domain, and cleavage at a specific site between the domains frees the two fragments. Our NMR analysis indicates that most residues of the prion domain are in fact disordered in the soluble form of Ure2p. Deleting the tether holding the C-terminal structured region to the amyloid core does not impair prion formation, arguing against steric impairment of amyloid formation. These results suggest that the N-terminal prion domain is unstructured in the soluble protein and does not have a specific interaction with the C-terminus.     

Is the signal from the mesophyll to the guard cells a vapour‐phase ion?

Previous studies have suggested that the red light and CO₂ responses of stomata are caused by a signal from the mesophyll to the guard cells. Experiments were conducted to test the idea that this signal is a vapour‐phase ion. Stomata in isolated epidermes of Tradescantia pallida were found to respond to air ions created by an electrode that was positioned under the epidermes. Anthocyanins in the epidermes of this species were observed to change colour in response to these air ions, and this change in colour was attributed to changes in pH. A similar change in lower epidermal colour was observed in intact leaves upon illumination and with changes in CO₂ concentration. Based on the change in epidermal colour, the pH of the epidermis was estimated to be approximately 7.0 in darkness and 6.5 in the light. Stomata in isolated epidermes responded to pH when suspended over (but not in contact with) solutions of different pH. We speculate that stomatal responses to CO₂ and light are caused by vapour‐phase ions, possibly hydronium ions that change the pH of the epidermis.     

Is there anionic ATPase in the nuclei of animal cells?

The nuclei of the rat liver, heart, thymus and of the mouse liver isolated in sucrose gradient reveal ATPase sensitive to bicarbonate, sulfite, azide and thiocyanate. The admixture of mitochondria and submitochondrial particles in the nuclear preparation was found negligible, which could not contribute to the anion ATPase in the nuclei. This was demonstrated by the calculation and by the introducing of mitochondria into the nuclear preparations.     

Is sparse and distributed the coding goal of simple cells?

The question of why the receptive fields of simple cells in the primary visual cortex are Gabor-like is a crucial one in vision research. Many research efforts (Olshausen and Field 1996, 1997; van Hateren and Ruderman 1998; van Hateren and van der Schaaf 1998) that yield a set of localized, oriented, and bandpass Gabor-like receptive fields believe that sparse and distributed is the coding goal of simple cells. This paper investigates a more general coding strategy that measures equally any departure from normality in the simple cells responses. That is, we investigate the possibility that highly kurtotic response histograms may result if simple cells explicitly seek, not maximally kurtotic, but rather maximally non-Gaussian response histograms to natural images. It is found that, under this coding strategy, the simulations produce a majority of localized, oriented, bandpass (Gabor-like) receptive fields. Some receptive fields, however, are spatially distributed and show little oriented structure. Nearly all receptive fields, regardless of whether they are Gabor-like or non-Gabor-like, yield highly kurtotic response histograms to natural images. Thus, in seeking maximally non-Gaussian response histograms, receptive fields spontaneously yield highly kurtotic histograms. The presence in our ensemble of nonlocalized, nonoriented receptive fields may be due to the artificial requirement that receptive fields be orthonormal. We conclude that the high kurtoses observed in the response histograms of simple-cell receptive fields to natural images may reflect a property of natural images themselves rather than an explicit coding goal used to structure simple-cell receptive fields.Acknowledgement This work was supported by the US Office of Naval Research under agreement number N68936-00-2-0002.     

Is the nuclear matrix the site of DNA replication in eukaryotic cells?

Four types of experiment were carried out to test the recently proposed model of matrix-bound replication in eukaryotic cells. In experiments with pulse-labelling we found preferential association of newly replicated DNA with the matrix only when the procedure for isolation includes first high-salt treatment of isolated nuclei and then digestion with nucleases, or when prior to digestion the nuclei have been stored for a prolonged time. In both cases, however, evidence was found that this preferential association is due to a secondary, artifactual binding of the newly replicated chromatin region to the matrix elements. Pulse-chase experiments and experiments with continuous labelling were carried out to answer the question whether during replication the DNA is reeled through the replication complexes, i.e., whether newly replicated DNA is temporarily or permanently associated with the matrix. The results showed that at that time the matrix DNA does not move from its site of attachment. Since, according to the model of matrix-bound replication, the forks are assumed to be firmly anchored to high-salt resistant proteinaceous matrix structures, the chromatin fragments isolated with endonuclease not recognizing newly replicated DNA and purified by sucrose gradient centrifugation should be free of replication intermediates. The electronmicroscopic analysis of such fragments revealed the existence of intact replication micro-bubbles. Moreover, the fragments with replication configurations appeared as smooth chromatin fibres not attached to elements characteristic for the matrix. All these experiments suggest that the nuclear skeleton is not a native site of DNA replication in eukaryotic cells.     

Microemboli-monitoring during the acute phase of ischemic stroke: Is it worth the time?

Background  

The prevalence of microembolic signals (MES) during the acute phase of ischemic stroke and its influence on outcome is not well studied. The aim of our study was to determine the prevalence of MES, the different factors that are associated with the presence of MES and the association between MES and outcomes in stroke patients investigated within 6 hours after the onset of ischemic stroke.     

Is the intrasomal phase of fast axonal transport driven by oscillations of intracellular calcium?

An hypothesis is presented suggesting that the delivery of vesicle-packaged protein from the neuronal soma to the axonal transport system is physiologically coupled to spontaneous fluctuations of intracellular calcium (Ca_i). Evidence is reviewed that oscillations of Ca_i, commonly detected as agonist-or voltage-triggered waves and spikes propagating through the cytosol, also occur as spontaneous events. Endogenously-generated oscillations are examined since intrasomal transport persists in the absence of extracellular signals or nerve impulse activity. Vesicle budding from the endoplasmic reticulum (ER) may be a key step at which anterograde transport is regulated by events related to the release and reuptake of ER stores of Ca²⁺.Special-issue dedicated to Dr. Sidney Ochs.     

Is the mechanical activity of epithelial cells controlled by deformations or forces?

The traction forces developed by cells depend strongly on the substrate rigidity. In this letter, we characterize quantitatively this effect on MDCK epithelial cells by using a microfabricated force sensor consisting in a high-density array of soft pillars whose stiffness can be tailored by changing their height and radius to obtain a rigidity range from 2 nN/microm up to 130 nN/microm. We find that the forces exerted by the cells are proportional to the spring constant of the pillars meaning that, on average, the cells deform the pillars by the same amount whatever their rigidity. The relevant parameter may thus be a deformation rather than a force. These dynamic observations are correlated with the reinforcement of focal adhesions that increases with the substrate rigidity.     

Is late replication of the inactive X chromosome irreversible in all cells of mammals?

The X chromosomes of the female bandicoot rat (Nesokia indica) were 3H-thymidine labeled during two consecutive cell divisions to determine if all of the same segments of the "triplicate-type" X chromosome of these animals always replicated late. In 87% of metaphases examined the findings were as expected. One entire X chromosome (X1) and the long arm of the other X (X2) synthesized DNA late in the S phase in both divisions. However, in the other 13% of the metaphases, the late-replicating and presumably genetically inactive short-arm segments of the X1 chromosome had completed DNA synthesis by the time it entered the late-S phase of the second cycle. Thus, in this species, some cells appear to have an X chromosome of which the facultative heteropycnotic segment condenses in one cell cycle but becomes euchromatic in the subsequent cell cycle. Although this appears at first to be inconsistent with the generally accepted pattern of X-chromosome condensation and genetic inactivation, it may represent an instance of evolutionary specialization for an as yet unexplained reason. It is also possible that closer analysis of other mammalian species with composite sex chromosomes or methods equally suitable for this type of analysis will reveal other instances where a minority of the somatic cells of females do not follow the predictions of the Lyons hypothesis completely.     

Is it really the “dark side” of herbal medicine?

正Aristolochic acids (AAs), previously rarely mentioned compounds, have been brought into the public eye several times since the beginning of this century; and currently, they have drawn even greater attention due to their association with liver cancer, as was recently reported by Ng et al.(Ng et al., 2017). The authors sequenced the whole exomes of 98patients with hepatocellular carcinomas (HCC) from Taiwan and reported that 78%of the cases carried the AAs mutational signature, A:TT:A transversion. Further examination of publicly available data from Chinese patients with HCC     

Is green fluorescent protein toxic to the living cells?

Green fluorescent protein (GFP) has become more popular to be used as a living marker for positively transfected clones in many studies. To establish stable cell lines constitutively expressing GFP, three GFPs expressed from plasmid pBIEGFP, pSG5GFP, and pRSGFP were introduced into NIH/3T3, BHK-21, Huh-7, and HepG2 cells. All the GFPs we used are the mutant forms of a common wild phenotype. The pBIEGFP expressed enhanced GFP (EGFP). The pRSGFP and pSG5GFP expressed red shift GFP (RSGFP). The RSGFP gene in pSG5GFP was driven by a strong SV40 promoter and showed at least 20-fold higher RSGFP expression by western blot analysis. Despite of the variation in the levels of GFP expression, many GFP expressing cells contracted, rounded-up, and died, which was confirmed by decreasing luciferase activity. CPP32 activity and flow cytometric analyses further demonstrate that cells expressing GFP underwent apoptosis. Our observation is contradictory to other reports that GFP is nontoxic to the cells. Most importantly, this paper shows for the first time the link between expression of GFP and induction of apoptosis. This finding should promote studies of GFP cytotoxicity and attempts to isolate new non-toxic mutants of GFP.     

Is inflammation the cause of pre-eclampsia?

It has been proposed that either excessive inflammation or an imbalance in angiogenic factors cause pre-eclampsia. In the present review, the arguments for and against the role of inflammation and/or angiogenic imbalance as the cause of pre-eclampsia are discussed on the basis of the Bradford-Hill criteria for disease causation. Although both angiogenic imbalance and systemic inflammation are implicated in pre-eclampsia, the absence of temporality of inflammatory markers with pre-eclampsia challenges the concept that excessive inflammation is the cause of pre-eclampsia. In contrast, the elevation of anti-angiogenic factors that precede the clinical signs of pre-eclampsia fulfils the criterion of temporality. The second most important criterion is the dose-response relationship. Although such a relationship has not been proven between pro-inflammatory cytokines and pre-eclampsia, high levels of anti-angiogenic factors have been shown to correlate with increased incidence and disease severity, hence satisfying this condition. Finally, as the removal of circulating sFlt-1 (soluble Fms-like tyrosine kinase receptor-1) from pre-eclamptic patients significantly improves the clinical outcome, it fulfils the Hill's experiment principle, which states that removal of the cause by an appropriate experimental regimen should ameliorate the condition. In contrast, treatment with high doses of corticosteroid fails to improve maternal outcome in pre-eclampsia, despite suppressing inflammation. Inflammation may enhance the pathology induced by the imbalance in the angiogenic factors, but does not by itself cause pre-eclampsia. Development of therapies based on the angiogenic and cytoprotective mechanisms seems more promising.     

What Is the Tree of Life?

A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic.One of the several ways in which microbiology puts the neo-Darwinian synthesis in jeopardy is by the threatening to “uproot the Tree of Life (TOL)” [1]. Lateral gene transfer (LGT) is much more frequent than most biologists would have imagined up until about 20 years ago, so phylogenetic trees based on sequences of different prokaryotic genes are often different. How to tease out from such conflicting data something that might correspond to a single, universal Tree of Life becomes problematic. Moreover, since many important evolutionary transitions involve lineage fusions at one level or another, the aptness of a tree (a pattern of successive bifurcations) as a summary of life’s history is uncertain [2–4].     

Are interstitial cells of Cajal plurifunction cells in the gut?

The proposed functions of the interstitial cells of Cajal (ICC) are to 1) pace the slow waves and regulate their propagation, 2) mediate enteric neuronal signals to smooth muscle cells, and 3) act as mechanosensors. In addition, impairments of ICC have been implicated in diverse motility disorders. This review critically examines the available evidence for these roles and offers alternate explanations. This review suggests the following: 1) The ICC may not pace the slow waves or help in their propagation. Instead, they may help in maintaining the gradient of resting membrane potential (RMP) through the thickness of the circular muscle layer, which stabilizes the slow waves and enhances their propagation. The impairment of ICC destabilizes the slow waves, resulting in attenuation of their amplitude and impaired propagation. 2) The one-way communication between the enteric neuronal varicosities and the smooth muscle cells occurs by volume transmission, rather than by wired transmission via the ICC. 3) There are fundamental limitations for the ICC to act as mechanosensors. 4) The ICC impair in numerous motility disorders. However, a cause-and-effect relationship between ICC impairment and motility dysfunction is not established. The ICC impair readily and transform to other cell types in response to alterations in their microenvironment, which have limited effects on motility function. Concurrent investigations of the alterations in slow-wave characteristics, excitation-contraction and excitation-inhibition couplings in smooth muscle cells, neurotransmitter synthesis and release in enteric neurons, and the impairment of the ICC are required to understand the etiologies of clinical motility disorders.     

Is the ClC-2 chloride channel involved in the Cl- secretory mechanism of gastric parietal cells?

It has been controversial whether the ClC-2 chloride channel is involved in hydrochloric acid secretion of gastric parietal cells. Here, we investigated whether ClC-2 is the apical Cl- channel associated with gastric acid secretion. Two anti-ClC-2 antibodies used in this study reacted with cloned ClC-2 protein expressed in HEK293 cells. In isolated rabbit gastric glands, significant expression of ClC-2 mRNA was observed, but the presence of ClC-2 protein was not clear. Furthermore, no expression of ClC-2 protein was observed in isolated rat and human gastric mucosa. Immunohistochemistry on the rat gastric mucosa showed no significant expression of ClC-2 protein in the parietal cells which showed abundant expression of H+,K+-ATPase. These results indicate that ClC-2 may not be a Cl- -transporting protein for gastric acid secretion in parietal cells.