Preventive therapies: weighing the pros and cons.

The author comments on three issues raised by Dr. Kenneth G. Marshall in his series on the benefits and harms of preventive therapies, which begins in this issue on page 1493. First, because the method by which the results of clinical trials are presented markedly affects the perception of those results some measure of absolute benefit and harm must be used when the results of clinical trials are presented. Second, there is increasing interest in decision aids as a means of helping patients to understand evidence and make therapeutic choices. It is important that these aids undergo rigorous testing before they are adopted for common use. Third, evidence-based clinical practice guidelines are a welcome resource for busy clinicians. However, physicians and patients should bear in mind that interpretations of the available evidence can vary, leading to different conclusions about the appropriateness of preventive therapies.     

Bacteriophages in dairy products: pros and cons

Since the time bacteriophages were first identified as a major cause of fermentation failure in the dairy industry, researchers have been struggling to develop strategies to exclude them from the dairy environment. Over 70 years of research has led to huge improvements in the consistency and quality of fermented dairy products, while also facilitating an appreciation of the beneficial properties of bacteriophages with respect to dairy product development. With specific reference to Lactococcus lactis and cheese production, this review outlines some recently reported novel methods aimed at limiting the bacteriophage infection as well as highlighting some beneficial aspects of bacteriophage activity.     

Traction fibres in chromosome movement: the pros and cons

The current discussion on the mechanism of chromosome movement in anaphase is dominated by a new hypothesis assuming active movement of the chromosome along stationary kinetochore microtubules. The aim of this article is to call attention to several older as well as to more recent observations on spindle structural dynamics and microtubule rearrangements which, in the author's opinion, cannot be explained by the new model. In fact, the observations seem to be more consistent with the classical concept of a traction fibre. For this reason, these observations should not be disregarded.     

Discontinuous native protein gel electrophoresis: pros and cons

A new native protein gel system was recently developed that enables the rapid and convenient analysis of virtually all soluble proteins, in particular including basic proteins, in their native oligomeric states. This gel system combines the addition of negative charges to the proteins by the dye SERVA Blue G with a Tris-histidine discontinuous buffer system and the use of polyacrylamide gradient gels. The use of histidine for sample focusing rather than glycine as a slow dipolar ion following from the cathode buffer serves to improve migration of basic proteins. In this review, the principle of function as well as the advantages and disadvantages of the new gel system are discussed in the context of other native protein gel systems and further methods for the analysis of the oligomeric state of a protein.     

Cytosine methylation: remaining faithful

DNA methyltransferase-1 (DNMT1) has a higher specific activity on hemimethylated DNA than on unmethylated DNA, but this preference is too small to explain the faithful mitotic inheritance of genomic methylation patterns. New genetic studies in plants and mammals have identified a novel factor that increases the fidelity of maintenance methylation.     

Heat stress in grapevine: the pros and cons of acclimation

Heat stress is a major limiting factor of grapevine production and quality. Acclimation and recovery are essential to ensure plant survival, and the recovery mechanisms can be independent of the heat response mechanisms. An experimental set up with and without acclimation to heat followed by recovery [stepwise acclimation and recovery (SAR) and stepwise recovery (SR), respectively] was applied to two grapevine varieties, Touriga Nacional (TN), and Trincadeira (TR), with different tolerance to abiotic stress. Major differences were found between leaves of SAR and SR, especially after recovery; in SAR, almost all parameters returned to basal levels while in SR they remained altered. Acclimation led to a swifter and short‐term antioxidative response, affecting the plant to a lesser extent than SR. Significant differences were found among varieties: upon stress, TN significantly increased ascorbate and glutathione reduction levels, boosting the cell's redox‐buffering capacity, while TR needed to synthesize both metabolites, its response being insufficient to keep the redox state at working levels. TR was affected by stress for a longer period and the up‐regulation pattern of antioxidative stress genes was more obvious. In TN, heat shock proteins were significantly induced, but the canonical heat‐stress gene signature was not evident probably because no shutdown of the housekeeping metabolism was needed.     

Messages in spike timing-dependent plasticity: pros and cons

Spike-timing dependent plasticity (STDP), a synaptic modification depending on a relative timing of presynaptic and postsynaptic spikes, has fascinated researchers in the fields of neurophysiology and computational neuroscience, because it is not only conceptually simple or biologically reasonable but is also versatile in neural network simulations. The STDP rule may be valid only under specific conditions, however. We propose herein a method that could find more natural and potent rules of synaptic plasticity.     

Correlation versus gradient type motion detectors: the pros and cons

Visual motion contains a wealth of information about self-motion as well as the three-dimensional structure of the environment. Therefore, it is of utmost importance for any organism with eyes. However, visual motion information is not explicitly represented at the photoreceptor level, but rather has to be computed by the nervous system from the changing retinal images as one of the first processing steps. Two prominent models have been proposed to account for this neural computation: the Reichardt detector and the gradient detector. While the Reichardt detector correlates the luminance levels derived from two adjacent image points, the gradient detector provides an estimate of the local retinal image velocity by dividing the spatial and the temporal luminance gradient. As a consequence of their different internal processing structure, both the models differ in a number of functional aspects such as their dependence on the spatial-pattern structure as well as their sensitivity to photon noise. These different properties lead to the proposal that an ideal motion detector should be of Reichardt type at low luminance levels, but of gradient type at high luminance levels. However, experiments on the fly visual systems provided unambiguous evidence in favour of the Reichardt detector under all luminance conditions. Does this mean that the fly nervous system uses suboptimal computations, or is there a functional aspect missing in the optimality criterion? In the following, I will argue in favour of the latter, showing that Reichardt detectors have an automatic gain control allowing them to dynamically adjust their input–output relationships to the statistical range of velocities presented, while gradient detectors do not have this property. As a consequence, Reichardt detectors, but not gradient detectors, always provide a maximum amount of information about stimulus velocity over a large range of velocities. This important property might explain why Reichardt type of computations have been demonstrated to underlie the extraction of motion information in the fly visual system under all luminance levels.     

Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax

Background

Cytosine methylation of DNA is conserved across eukaryotes and plays important functional roles regulating gene expression during differentiation and development in animals, plants and fungi. Hydroxymethylation was recently identified as another epigenetic modification marking genes important for pluripotency in embryonic stem cells.

Results

Here we describe de novo cytosine methylation and hydroxymethylation in the ciliate Oxytricha trifallax. These DNA modifications occur only during nuclear development and programmed genome rearrangement. We detect methylcytosine and hydroxymethylcytosine directly by high-resolution nano-flow UPLC mass spectrometry, and indirectly by immunofluorescence, methyl-DNA immunoprecipitation and bisulfite sequencing. We describe these modifications in three classes of eliminated DNA: germline-limited transposons and satellite repeats, aberrant DNA rearrangements, and DNA from the parental genome undergoing degradation. Methylation and hydroxymethylation generally occur on the same sequence elements, modifying cytosines in all sequence contexts. We show that the DNA methyltransferase-inhibiting drugs azacitidine and decitabine induce demethylation of both somatic and germline sequence elements during genome rearrangements, with consequent elevated levels of germline-limited repetitive elements in exconjugant cells.

Conclusions

These data strongly support a functional link between cytosine DNA methylation/hydroxymethylation and DNA elimination. We identify a motif strongly enriched in methylated/hydroxymethylated regions, and we propose that this motif recruits DNA modification machinery to specific chromosomes in the parental macronucleus. No recognizable methyltransferase enzyme has yet been described in O. trifallax, raising the possibility that it might employ a novel cytosine methylation machinery to mark DNA sequences for elimination during genome rearrangements.     

Absolute nannofossil abundance estimates: Quantifying the pros and cons of different techniques

A quick and inexpensive method to determine absolute nannofossil abundance in deep sea sediments – the “drop” technique (modified dilution method) – was compared to two other available methods – the filtration and random settling techniques. All techniques rely on the same basic principle, under which a volume of known concentration (bulk sediment weight/mL) is distributed evenly over a known total area (glass slide or filter) to then count particles within a set of (randomly) selected fields of view. The three preparation techniques were also calibrated by spiking the samples with microbeads to approach the “real values” as closely as possible. Significant offsets in abundance estimates between methods mainly reflect bias due to the uneven distribution and/or loss of particles. We show that the drop technique is most consistent and accurate in estimating “real values” and offers similar or better reproducibility than the other techniques. The drop method also allows detection of the same trends with or without calibration with microbeads. The filtration method holds the risk to drastically underestimate absolute abundances, while the settling technique is demanding in terms of time and may suffer from advection processes. The composition of nannofossil assemblages can be reliably determined by any of the three different techniques.     

The pros and cons of interferons for oncolytic virotherapy

Interferons (IFN) are potent immune stimulators that play key roles in both innate and adaptive immune responses. They are considered the first line of defense against viral pathogens and can even be used as treatments to boost the immune system. While viruses are usually seen as a threat to the host, an emerging class of cancer therapeutics exploits the natural capacity of some viruses to directly infect and kill cancer cells. The cancer-specificity of these bio-therapeutics, called oncolytic viruses (OVs), often relies on defective IFN responses that are frequently observed in cancer cells, therefore increasing their vulnerability to viruses compared to healthy cells. To ensure the safety of the therapy, many OVs have been engineered to further activate the IFN response. As a consequence of this IFN over-stimulation, the virus is cleared faster by the immune system, which limits direct oncolysis. Importantly, the therapeutic activity of OVs also relies on their capacity to trigger anti-tumor immunity and IFNs are key players in this aspect. Here, we review the complex cancer–virus–anti-tumor immunity interplay and discuss the diverse functions of IFNs for each of these processes.     

The pros and cons of autophagic flux among herpesviruses

Autophagy has been intensively studied in herpes simplex virus type 1 (HSV-1), a human alphaherpesvirus. The HSV-1 genome encodes a well-known neurovirulence protein called ICP34.5. When the gene encoding this protein is deleted from the genome, the virus is markedly less virulent when injected into the brains of animal models. Subsequent characterization of ICP34.5 established that the neurovirulence protein interacts with BECN1, thereby inhibiting autophagy and facilitating viral replication in the brain. However, an ortholog of the ICP34.5 gene is lacking in the genomes of other closely related alphaherpesviruses, such as varicella-zoster virus (VZV). Further, autophagosomes are easily identified in the exanthem (rash) that is the hallmark of both VZV diseases—varicella and herpes zoster. Inhibition of autophagy leads to diminished VZV titers. Finally, no block is detected in studies of autophagic flux following VZV infection. Thus autophagy appears to be proviral during VZV infection while antiviral during HSV-1 infection. Because divergence to this degree is extremely unusual for 2 closely related herpesviruses, we postulate that VZV has accommodated its infectious cycle to benefit from autophagic flux, whereas HSV-1 has captured cellular immunomodulatory genes to inhibit autophagy.     

Parthenogenesis in mammals: pros and cons in pluripotent cell derivation

Embryonic stem cells (ESCs) represent a useful tool for cell therapy studies, however the use of embryos for their derivation give rise to ethical, religious and legal problems when applied to the human. During the last years parthenogenesis has been proposed as an alternative source to obtain ESCs. Based on the fact that parthenotes avoid many concerns surrounding the “ad hoc” in vitro production and following destruction of viable human embryos. Unfortunately many aspects related to parthenogenetic cell biology are not fully understood and still need to be elucidated. In this review we describe advantages and limits of these cells. We discuss their typical ESC morphology and high telomerase activity, which disappears after differentiation. We examine the pluripotency signature that they share with bi-parental ESCs. We review their high differentiation plasticity that allow for the derivation of several mature cell type populations when we expose these cells to adequate conditions. On the other hand, in-depth analysis demonstrated chromosome mal-segregation and altered mechanisms controlling centriole arrangement and mitotic spindle formation in these cells. We hypothesize their monoparental origin as one of the possible cause of these anomalies and suggest a great caution if a therapeutic use is considered.