Non-equivalent interactions between amino-terminal domains of neighboring lambda integrase protomers direct Holliday junction resolution

The bacteriophage lambda site-specific recombinase (Int), in contrast to other family members such as Cre and Flp, has an amino-terminal domain that binds "arm-type" DNA sequences different and distant from those involved in strand exchange. This defining feature of the heterobivalent recombinases confers a directionality and regulation that is unique among all recombination pathways. We show that the amino-terminal domain is not a simple "accessory" element, as originally thought, but rather is incorporated into the core of the recombination mechanism, where it is well positioned to exert its profound effects. The results reveal an unexpected pattern of intermolecular interactions between the amino-terminal domain of one protomer and the linker region of its neighbor within the tetrameric Int complex and provide insights into those features distinguishing an "active" from an "inactive" pair of Ints during Holliday junction resolution.     

NMDA-responsible, APV-insensitive receptor in cultured human astrocytes

The present study was conducted to assess N-methyl-D-aspartate (NMDA)-responsible receptors in cultured human astrocytes by monitoring whole-cell membrane currents. NMDA generated currents, that are potentiated by glycine and blocked by Mg2+, with the current/voltage relation showing a reversal potential of +/- 0 mV. The currents were not inhibited by either the selective NMDA receptor antagonist, D-2-amino-5-phosphonovaleric acid (APV), or the non-selective ionotropic glutamate receptor antagonist, kynurenic acid. The currents were inhibited only by 19% in Ca2+-free extracellular solution. Furthermore, GDPbetaS, a broad G-protein inhibitor, inhibited NMDA-induced currents to 82% of original levels. The results of the present study thus suggest that an NMDA-responsible, APV-insensitive receptor with low Ca2+ permeability, distinct from the neuronal NMDA receptors, is expressed in human astrocytes and that the receptor is regulated in part by an unknown G-protein-linked receptor.     

Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: A modeling study

BackgroundDevelopment of an effective antiviral drug for Coronavirus Disease 2019 (COVID-19) is a global health priority. Although several candidate drugs have been identified through in vitro and in vivo models, consistent and compelling evidence from clinical studies is limited. The lack of evidence from clinical trials may stem in part from the imperfect design of the trials. We investigated how clinical trials for antivirals need to be designed, especially focusing on the sample size in randomized controlled trials.Methods and findingsA modeling study was conducted to help understand the reasons behind inconsistent clinical trial findings and to design better clinical trials. We first analyzed longitudinal viral load data for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) without antiviral treatment by use of a within-host virus dynamics model. The fitted viral load was categorized into 3 different groups by a clustering approach. Comparison of the estimated parameters showed that the 3 distinct groups were characterized by different virus decay rates (p-value < 0.001). The mean decay rates were 1.17 d⁻¹ (95% CI: 1.06 to 1.27 d⁻¹), 0.777 d⁻¹ (0.716 to 0.838 d⁻¹), and 0.450 d⁻¹ (0.378 to 0.522 d⁻¹) for the 3 groups, respectively. Such heterogeneity in virus dynamics could be a confounding variable if it is associated with treatment allocation in compassionate use programs (i.e., observational studies).Subsequently, we mimicked randomized controlled trials of antivirals by simulation. An antiviral effect causing a 95% to 99% reduction in viral replication was added to the model. To be realistic, we assumed that randomization and treatment are initiated with some time lag after symptom onset. Using the duration of virus shedding as an outcome, the sample size to detect a statistically significant mean difference between the treatment and placebo groups (1:1 allocation) was 13,603 and 11,670 (when the antiviral effect was 95% and 99%, respectively) per group if all patients are enrolled regardless of timing of randomization. The sample size was reduced to 584 and 458 (when the antiviral effect was 95% and 99%, respectively) if only patients who are treated within 1 day of symptom onset are enrolled. We confirmed the sample size was similarly reduced when using cumulative viral load in log scale as an outcome.We used a conventional virus dynamics model, which may not fully reflect the detailed mechanisms of viral dynamics of SARS-CoV-2. The model needs to be calibrated in terms of both parameter settings and model structure, which would yield more reliable sample size calculation.ConclusionsIn this study, we found that estimated association in observational studies can be biased due to large heterogeneity in viral dynamics among infected individuals, and statistically significant effect in randomized controlled trials may be difficult to be detected due to small sample size. The sample size can be dramatically reduced by recruiting patients immediately after developing symptoms. We believe this is the first study investigated the study design of clinical trials for antiviral treatment using the viral dynamics model.

Using a viral dynamics model, Shingo Iwami and colleagues investigate the sample sizes required to detect significant antiviral drug effects on COVID-19 in randomized controlled trials.     

Dual coding hypotheses for neural information representation

Information is represented and processed in neural systems in various ways. The rate coding, population coding, and temporal coding are typical examples of representation. It is a hot issue in neuroscience what kinds of coding is used in real neural systems. Different regions of the brain may resort to different coding strategies. Moreover, recent studies suggest the possibility of dual or multiple codes, in which different modes of information are embedded in one neural system. The present paper reviews various possibilities of neural codes focusing on dual codes.     

Redundancy reducing processes in single neurons

Interaction mechanisms between excitatory and inhibitory impulse sequences operating on neurons play an important role for the processing of information by the nervous system. For instance, the convergence of excitatory and inhibitory influences on retinal ganglion cells to form their receptive fields has been taken as an example for the process of neuronal sharpening by lateral inhibition. In order to analyze quantitatively the functional behavior of such a system, Shannon's entropy method for multiple access channels has been applied to biological two-inputs-one-output systems using the theoretical model developed by Tsukada et al. (1979). Here we give an extension of this procedure from the point of view to reduce redundancy of information in the input signal space of single neurons and attempt to obtain a new interpretation for the information processing of the system. The concept for the redundancy reducing mechanism in single neurons is examined and discussed for the following two processes. The first process is concerned with a signal space formed by superposing two random sequences on the input of a neuron. In this process, we introduce a coding technique to encode the inhibitory sequence by using the timing of the excitatory sequence, which is closely related to an encoding technique of multiple access channels with a correlated source (Marko, 1966, 1970, 1973; Slepian and Wolf, 1973) and which is an invariant transformation in the input signal space without changing the information contents of the input. The second process is concerned with a procedure of reducing redundant signals in the signal space mentioned before. In this connection, it is an important point to see how single neurons reduce the dimensionality of the signal space via transformation with a minimum loss of effective information. For this purpose we introduce the criterion that average transmission of information from signal space to the output does not change when redundant signals are added. This assumption is based on the fact that two signals are equivalent if and only if they have identical input-output behavior. The mechanism is examined and estimated by using a computer-simulated model. As the result of such a simulation we can estimate the minimal segmentation in the signal space which is necessary and sufficient for temporal pattern sensitivity in neurons.     

Inhibition of 15-hydroxy prostaglandin dehydrogenase and increase of prostaglandin E2: effect of sofalcone on rat gastric mucosa

The effect of sofalcone, an anti-ulcer agent, on gastric mucosal prostaglandin (PG) metabolism was studied. Gastric mucosal PGE2 was determined in rats in which PGE2 synthesis was inhibited by preadministration of indomethacin. Oral administration of sofalcone at doses of 200 and 400 mg/kg significantly inhibited the PG metabolizing enzyme, 15-hydroxy-PG-dehydrogenase (15-OH-PG-DH) activity and increased PGE2 contents in the rat gastric mucosa. The inhibition of 15-OH-PG-DH activity was accompanied by an increase of PGE2 contents up to 6 hours after the administration of sofalcone. These changes, however, were not observed 12 hours after its administration. Intraperitoneally administered sofalcone also inhibited 15-OH-PG-DH activity and increased PGE2 content. The inhibition of 15-OH-PG-DH activity by sofalcone was noncompetitive and uncompetitive against substrates NAD and PGE1, respectively. These results suggest that the increase of the gastric PGE2 level is mainly due to the inhibition of 15-OH-PG-DH activity, and this increase in PGE2 may be involved in the anti-ulcer effect of sofalcone.     

The Striated Bands of Paramecium Are Immunologically Distinct from the Centrin-Specific Infraciliary Lattice and Cytostomal Cord

The pellicle of Paramecium has three two-dimensionally arrayed systems that occupy separate but closely paralleling planes. All three systems are now distinguishable by their differing immunological properties. This study focused on the two deeper systems. The infraciliary lattice lies innermost and labels with centrin-specific antibodies. The middle system, the striated bands, is specifically labeled with a monoclonal antibody that we have raised to a 110 kDa conical antigen in P. multimicronucleatum. This antibody labels a similar geometric cortical pattern in at least two species, P. multimicronucleatum and P. tetraurelia. Centrin-specific structures appear to be net-like in the above two species but show a more interrupted pattern in P. caudatum. The cytostomal cord is an essentially unbranched extension of the net-like infraciliary lattice and, like it, is centrin-specific. The cord has a unique association with the alveolar sacs which suggest these calcium-storing compartments contribute to the calcium fluxes required for contraction of the cord. A structural rather than a contractile function is favored for the striated bands, based solely on their morphology.     

Stochastic synchronization of genetic oscillator networks

Background  

The study of synchronization among genetic oscillators is essential for the understanding of the rhythmic phenomena of living organisms at both molecular and cellular levels. Genetic networks are intrinsically noisy due to natural random intra- and inter-cellular fluctuations. Therefore, it is important to study the effects of noise perturbation on the synchronous dynamics of genetic oscillators. From the synthetic biology viewpoint, it is also important to implement biological systems that minimizing the negative influence of the perturbations.