Abstract biological systems as sequential machines

It is shown that a rather close relationship exists between the (ℳ,ℛ)-systems, defined previously as prototypes of abstract biological systems, and the sequential machines which have been studied by various authors. The theory of sequential machines is reformulated in a way suitable for its application to the study of the intertransformability of (ℳ,ℛ)-systems as a result of environmental alteration. The important concept of strong connectedness is most useful in this direction, and is used to derive a number of results on intertransformability. Some suggestions are made for further studies along these lines.     

Abstract biological systems as sequential machines: Behavioral reversibility

Rosen’s identification of abstract biological systems, called (M,R)-systems, with sequential machines is formally characterized. It is then shown that the determination of environmental alterations of (M,R)-systems from a knowledge of the response sequence and the structure of the system, which we call behavioral reversibility, can be interpreted as information-losslessness of sequential machines. Applying this relationship, necessary conditions for behavioral reversibility are derived. It is further shown that, similar to Rosen’s work on structural reversibility, (M,R)-systems are behaviorally reversible only if the number of physically realizable mappings are restricted.     

Abstract biological systems as sequential machines II: Strong connectedness and reversibility

It was previously shown that the abstract biological systems called. (ℳ, ℛ)-systems could be regarded formally as sequential machines, and that when this was done, the reversibility of environmentally induced structural changes in these systems was closely related to the strong connectedness of the corresponding machines. In the present work it is shown that the sequential machines arising in this way are characterized by the property that the size of the input alphabet is very small compared with the size of the set of states of the machine. It is further shown that machines with this property almost always fail to be strongly connected. Therefore, it follows that one of the following alternatives holds: either most environmentally induced structural alterations are not environmentally reversible, or else many mappings in the category from which the (ℳ, ℛ)-systems are formed must not be physically realizable.     

Abstract biological systems as sequential machines: III. Some algebraic aspects

Using the relationship between (M,R) and sequential machines developed in previous work, it is shown that the totality of (M,R) which can be formed over a given categoryA itself forms a category in a natural fashion.     

Cellular systems as graphs

The definition of an (M,R) is formulated in a way that emphasizes its mathematical properties. Neglecting interactions between the components, it is shown that:

1. An (M,R) contains only one non-reestablishable component.
2. If an (M,R) contains only one non-reestablishable component, then that component is central.

Examples are given to illustrate the biological significance of these two results. The notion of “lag-independence” is introduced, and it is shown that if a system possesses only one non-reestablishable component which is “lag-independent” then all components are lag-independent. The concepts of reestablishability, centrality and lag-independence are applied in order to suggest various criteria for optimal organization of (M,R).     

Bacterial Type IV secretion systems: versatile virulence machines

Many bacterial pathogens employ multicomponent protein complexes to deliver macromolecules directly into their eukaryotic host cell to promote infection. Some Gram-negative pathogens use a versatile Type IV secretion system (T4SS) that can translocate DNA or proteins into host cells. T4SSs represent major bacterial virulence determinants and have recently been the focus of intense research efforts designed to better understand and combat infectious diseases. Interestingly, although the two major classes of T4SSs function in a similar manner to secrete proteins, the translocated 'effectors' vary substantially from one organism to another. In fact, differing effector repertoires likely contribute to organism-specific host cell interactions and disease outcomes. In this review, we discuss the current state of T4SS research, with an emphasis on intracellular bacterial pathogens of humans and the diverse array of translocated effectors used to manipulate host cells.     

Stability of membrane systems modeled as multilayered viscoelastic films

We have modeled interacting plane-parallel membranes as viscoelastic multilayered films. A linear dynamic analysis was used. It gave the general conditions for stability of membrane systems having an arbitrary number of membranes and films. The particular cases of one, two and three interacting layers were considered in detail. The results suggest a strong dependence of the stability of membrane systems on the interfacial tensions and the thickness of individual membranes and films and rather weak dependence on their viscosities and elasticities. The theoretical predictions are in semi-quantitative agreement with data on electrically induced membrane fusion in dielectrophoresis.     

Cellular degradation systems in ferroptosis

In eukaryotic cells, macromolecular homeostasis requires selective degradation of damaged units by the ubiquitin-proteasome system (UPS) and autophagy. Thus, dysfunctional degradation systems contribute to multiple pathological processes. Ferroptosis is a type of iron-dependent oxidative cell death driven by lipid peroxidation. Various antioxidant systems, especially the system xc⁻-glutathione-GPX4 axis, play a significant role in preventing lipid peroxidation-mediated ferroptosis. The endosomal sorting complex required for transport-III (ESCRT-III)–dependent membrane fission machinery counteracts ferroptosis by repairing membrane damage. Moreover, cellular degradation systems play a dual role in regulating the ferroptotic response, depending on the cargo they degrade. The key ferroptosis repressors, such as SLC7A11 and GPX4, are degraded by the UPS. In contrast, the overactivation of selective autophagy, including ferritinophagy, lipophagy, clockophagy and chaperone-mediated autophagy, promotes ferroptotic death by degrading ferritin, lipid droplets, circadian proteins, and GPX4, respectively. Autophagy modulators (e.g., BECN1, STING1/TMEM173, CTSB, HMGB1, PEBP1, MTOR, AMPK, and DUSP1) also determine the ferroptotic response in a context-dependent manner. In this review, we provide an updated overview of the signals and mechanisms of the degradation system regulating ferroptosis, opening new horizons for disease treatment strategies.Subject terms: Cell biology, Molecular biology     

Kinesin motors as molecular machines

Molecular motor proteins, fueled by energy from ATP hydrolysis, move along actin filaments or microtubules, performing work in the cell. The kinesin microtubule motors transport vesicles or organelles, assemble bipolar spindles or depolymerize microtubules, functioning in basic cellular processes. The mechanism by which motor proteins convert energy from ATP hydrolysis into work is likely to differ in basic ways from man-made machines. Several mechanical elements of the kinesin motors have now been tentatively identified, permitting researchers to begin to decipher the mechanism of motor function. The force-producing conformational changes of the motor and the means by which they are amplified are probably different for the plus- and minus-end kinesin motors.     

Membrane transporters as machines: degenerate singularities as a requirement for function

It is suggested that Membrane Transporter functionality is based on low energy paths between proteins of different conformations. A simple extension of the Born-Oppenheimer approximation is used to reduce the protein structure problem to one of the kinematics of engineering mechanisms. Such low energy paths between conformations with the same handedness imply the existence of degenerate singularities in the engineering mechanism. The requirement for degeneracy leads to a number of conjectures. These include the structure and function of chaperones for constructing such proteins and the thermodynamic properties of membrane transporters.     

Cellular and circuit properties supporting different sensory coding strategies in electric fish and other systems

Neural codes often seem tailored to the type of information they must carry. Here we contrast the encoding strategies for two different communication signals in electric fish and describe the underlying cellular and network properties that implement them. We compare an aggressive signal that needs to be quickly detected, to a courtship signal whose quality needs to be evaluated. The aggressive signal is encoded by synchronized bursts and a predictive feedback input is crucial in separating background noise from the communication signal. The courtship signal is accurately encoded through a heterogenous population response allowing the discrimination of signal differences. Most importantly we show that the same strategies are used in other systems arguing that they evolved similar solutions because they faced similar tasks.     

Helicases as nucleic acid unwinding machines

Nucleic acid unwinding is an essential step in many biomolecular processes. Researchers in this field recently met to examine progress and outstanding issues.     

Stability and catalytic properties of penicillin acylase in systems with low water content

Stability and catalytic properties of native and immobilized penicillin acylase were studied in systems with low water content. Preparations of both native and immobilized penicillin acylase demonstrated the catalytic activity even in solid-phase systems which contained 3-5 wt. % of water. The stability and catalytic activity of penicillin acylase at low water content depended on the thermodynamic water activity (aw) in the system.     

时延细胞神经网络的全局稳定性分析

本文利用 Ｌｙａｐｕｎｏｖ泛函方法和一些分析技巧得到了一类时延细胞神经网络ＤＣＮＮ全局渐进稳定性的若干新的判据；这些判据可用于设计出全局稳定的各种动态网络，且在信号处理，特别是动态图象处理中具有重要的意义．     

Stability of large systems

We use the May-Wigner Stability Theorem (Geman (1984) preprint, Brown University; Hastings (1984) preprint, Hofstra University), to study the Lyapunov and structural stability of "real" large systems. Here are our new main results. For large systems which satisfy certain natural scaling relations (Harrison, Am. Natur., 113 (1979) 659; May (1979) Blackwell Scientific, Oxford), Lyapunov stability tends to increase with increasing complexity. However, at least one aspect of structural stability decreases: both competitive and cooperative effects can rapidly destabilize such a system. Finally, we observe that random matrices which satisfy the hypotheses and stability criterion of the May-Wigner theorem are asymptotically of the form 'rotation followed by multiplication by lambda,lambda less than 1'. This allows an easy analysis of the effects of noise in these systems. We conclude by briefly discussing applications to analysis of stability of systems such as the world economy, power networks, and the immune system.     

Stability of commensalistic systems

The response of two-species commensalistic systems in a chemostat has been investigated after perturbations in steady state conditions and after step changes in dilution rate. The system is inherently stable with not more than three overshoots and undershoots possible. More complicated commensalistic systems are less stable, with limit cycle response occurring after dilution rate changes when feedback inhibition and feedforward activation occurs. In general variation of feedback parameters is more effective in changing the behavior of the systems than variation of feedforward parameters. Limited agreement with the experimental data of Chao and Reilly was obtained.     

Stability of self-incompatibility systems

Summary Multi-locus self-incompatibility systems offer few obvious adaptive advantages to the species possessing them. However, the gametophytic system's independent gene action allows the separate genes in a two gene system to behave as if they were individually not involved in a systematic disruption of panmixia. Under such circumstances, fixation of one of the two genes is readily obtained if an allele possesses a selective advantage. The resulting single gene system (the classic Nicotiana system) is then resistant to disruption, except by genes which allow selfing, which rapidly reach fixation.