Reexamining assumptions about miRNA-guided gene silencing

MicroRNAs (miRNAs) are short endogenously expressed RNAs that have the potential to regulate the expression of any RNA. This potential has led to the publication of several thousand papers each year connecting miRNAs to many different genes and human diseases. By contrast, relatively few papers appear that investigate the molecular mechanism used by miRNAs. There is a disconnect between rigorous understanding of mechanism and the extraordinary diversity of reported roles for miRNAs. Consequences of this disconnect include confusion about the assumptions underlying the basic science of human miRNAs and slow development of therapeutics that target miRNAs. Here, we present an overview of investigations into miRNAs and their impact on gene expression. Progress in our understanding of miRNAs would be aided by a greater focus on the mechanism of miRNAs and a higher burden of evidence on researchers who seek to link expression of a particular miRNA to a biological phenotype.     

Control mechanisms of diel vertical migration: theoretical assumptions

We explore control mechanisms underlying the vertical migration of zooplankton in the water column under the predator-avoidance hypothesis. Two groups of assumptions in which the organisms are assumed to migrate vertically in order to minimize realized or effective predation pressure (type-I) and to minimize changes in realized or effective predation pressure (type-II), respectively, are investigated. Realized predation pressure is defined as the product of light intensity and relative predation abundance and the part of realized predation pressure that really affects organisms is termed as effective predation pressure. Although both types of assumptions can lead to the migration of zooplankton to avoid the mortality from predators, only the mechanisms based on type-II assumptions permit zooplankton to undergo a normal diel vertical migration (morning descent and evening ascent). The assumption of minimizing changes in realized predation pressure is based on consideration of DVM induction only by light intensity and predators. The assumption of minimizing changes in effective predation pressure takes into account, apart from light and predators also the effects of food and temperature. The latter assumption results in the same expression of migration velocity as the former one when both food and temperature are constant over water depth. A significant characteristic of the two type-II assumptions is that the relative change in light intensity plays a primary role in determining the migration velocity. The photoresponse is modified by other environmental variables: predation pressure, food and temperature. Both light and predation pressure are necessary for organisms to undertake DVM. We analyse the effect of each single variable. The modification of the phototaxis of migratory organisms depends on the vertical distribution of these variables.     

Analyzing protein-DNA recognition mechanisms

We present a computational algorithm that can be used to analyze the generic mechanisms involved in protein-DNA recognition. Our approach is based on energy calculations for the full set of base sequences that can be threaded onto the DNA within a protein-DNA complex. It is able to reproduce experimental consensus binding sequences for a variety of DNA binding proteins and also correlates well with the order of measured binding free energies. These results suggest that the crystal structure of a protein-DNA complex can be used to identify all potential binding sequences. By analyzing the energy contributions that lead to base sequence selectivity, it is possible to quantify the concept of direct versus indirect recognition and to identify a new concept describing whether the protein-DNA interaction and DNA deformation terms select optimal binding sites by acting in accord or in disaccord.     

Testing traditional assumptions about regional migration in bats

While some bats cover long distances during migration, moving thousands of kilometers, most migratory bats are considered regional migrants, thought to move relatively short distances (<?500 km) between hibernacula and maternity sites. However, behavior can vary considerably among species and our understanding of these movements has largely been limited to banding studies or detailed tracking of small numbers of bats by aircraft. Inferring population-wide behavior from small samples is difficult and can introduce bias. We tagged 108 Indiana bats (Myotis sodalis) in the Midwestern US and used a regional network of radiotelemetry receivers to study movement patterns. With this dataset, we tested the following traditional generalizations about regional migrants: (1) bats move away from hibernacula in spring in all directions with known maternity roosts, e.g., in a star-like pattern; (2) bats follow linear landscape features; (3) long-distance movements are uncommon; and (4) autumn migration comprises a single movement from summer maternity site to winter hibernaculum. In spring, bats left the hibernaculum immediately and primarily moved north despite available maternity roosts in all directions. We found no evidence that bats follow rivers, the predominant linear element in the landscape. Only six tagged bats traveled >?100 km, suggesting that longer-distance movements may be outliers. In autumn, only two bats visited multiple known hibernacula, and after swarming, some females moved >?100 km to areas without known hibernacula. Common generalizations about regional migrant movements may not be representative of population behavior and care should be taken with respect to management decisions based on those assumptions.     

Decision making and recognition mechanisms

Determining how individuals adjust their behaviour to maximize reproductive opportunities is fundamental to understanding the adaptive significance of behavioural variations. Such 'decision making' requires recognition mechanisms, whereby an individual evaluates cues that yield information about the potential reproductive outcomes of alternative behaviours. Here, we develop a quantitative model for understanding how individuals evaluate cues. Only when a proximate (immediate) cue predicts reproductive value more reliably than an evolved predisposition, will the cue influence an individual's decision. The model resolves some long-standing controversies in evolutionary biology involving recognition mechanisms and interpretations of behavioural decisions that were observed after manipulations of cues of parentage, kinship and mate quality.     

Neural mechanisms of object recognition

Single-unit recordings from behaving monkeys and human functional magnetic resonance imaging studies have continued to provide a host of experimental data on the properties and mechanisms of object recognition in cortex. Recent advances in object recognition, spanning issues regarding invariance, selectivity, representation and levels of recognition have allowed us to propose a putative model of object recognition in cortex.     

Innate mechanisms of viral recognition

Viruses are obligate parasites which can infect cells of all living organisms. Multiple antiviral defense mechanisms appeared early in the evolution of the immune system. Higher vertebrates possess the most complex antiviral immunity based on both innate and adoptive immune responses. However, a majority of living organisms, including plants and invertebrates, rely exclusively on innate immune mechanisms for protection against viral infections. There are some striking similarities in several components of innate immune recognition in mammals, plants, and insects suggesting that these signaling cascades are highly conserved in the evolution of the immune system. This review summarizes recent advances in the field of innate immune recognition of viruses, with a focus on pattern-recognition receptors.     

A rigorous approach to investigating common assumptions about disease transmission

Changing scale, for example, the ability to move seamlessly from an individual-based model to a population-based model, is an important problem in many fields. In this paper, we introduce process algebra as a novel solution to this problem in the context of models of infectious disease spread. Process algebra allows us to describe a system in terms of the stochastic behaviour of individuals, and is a technique from computer science. We review the use of process algebra in biological systems, and the variety of quantitative and qualitative analysis techniques available. The analysis illustrated here solves the changing scale problem: from the individual behaviour we can rigorously derive equations to describe the mean behaviour of the system at the level of the population. The biological problem investigated is the transmission of infection, and how this relates to individual interactions.     

The substrate recognition mechanisms in chaperonins

Chaperonins are a family of proteins devoted to assisting the folding of other proteins. They are large oligomers assembled into ring structures that enclose a cavity in which folding takes place. For this process to occur, the chaperonin must first recognize and interact with the unfolded polypeptide, then undergo a conformational change upon nucleotide binding that results in the closure of the cavity which in turn mediates the folding reaction inside the cavity. Although this general mechanism seems to apply to every chaperonin studied so far, there exist two different modes of interaction between the chaperonin and the substrate. The first occurs mainly through the interaction between the exposed hydrophobic residues of the unfolded polypeptides and those of the chaperonin substrate binding site, as elucidated for the chaperonin GroEL from E. coli. The second type of mechanism has been described so far only for the cytosolic chaperonin CCT (Chaperonin Containing TCP-1) and here the interaction seems to be of a more specific nature, involving charged and polar residues in both the chaperonin and the substrate, which interacts with CCT in a structured, quasi-native conformation.     

Codon recognition mechanisms in plant chloroplasts

In chloroplasts, all 61 sense codons are found in chloroplast (cp) DNA sequences coding for proteins. However among the sequenced cp tRNAs or tRNA genes, tRNAs with anticodons complementary to codons CUU/C (Leu), CCU/C (Pro), GCU/C (Ala) and CGC/A/G (Arg) [or CGC/A (Arg) in Marchantia] have not been found. In this paper we show that cp tRNA^Ala(U^*GC), cp tRNA^Pro(U^*GG) and cp tRNA^Arg(ICG) are able to decode the corresponding four-codon family. In the case of leucine codons CUU/C, we show that U:U and U:C wobble mechanisms can operate to allow the reading of these codons by cp tRNA^Leu (UAm⁷G).     

对荒漠的一些认识

阐述了荒漠的类型、基本成因、荒漠的限制因素(水)、重要的资源(热量)和导致沙漠流动的风,也谈及不合理开发可能导致的危害。强调遵循自然规律,合理利用资源,是防止荒漠化等一系列环境问题的途径。     

Visual mechanisms of recognition of vanishing figures

The acuity test Landolt C's with a complex contour imitating various kinds of high-pass spatial frequency filtering generated as a printed visual acuity charts with a grey background were studied with regard to recognition thresholds. Comparisons were made for recognition thresholds with different complex contours. When the vanishing optotypes are out of focus, their image on the retina fades rapidly into the grey background, rendering them invisible rather than merely blurred as in the standard chart. The data obtained confirm that the recognition distance depends on physical property of complex contour profile and show the importance of the Landolt C spatial frequency spectrum for recognition of different types of the complex contour.     

Chiral recognition mechanisms with macrocyclic glycopeptide selectors

Macrocyclic glycopeptide selectors are naturally occurring antibiotics produced by microorganisms. They were found to be excellent chiral selectors for a wide range of enantiomers, including amino acids. Four selectors are commercialized as chiral stationary phases (CSP) for chromatography. They are ristocetin, teicoplanin, vancomycin, and the teicoplanin aglycone (TAG). The key docking interaction for amino acid recognition was established to be a charge-charge interaction between the anionic carboxylate group of the amino acid and a cationic amine group of the macrocyclic peptidic selector basket. The carbohydrate units are responsible for secondary interactions. However, they hinder somewhat the charge-charge docking interaction. The TAG selector is more effective for amino acid enantioseparations than the other CSPs. The "sugar" units are however useful allowing for chiral recognitions of other analytes, e.g., beta-blockers, not possible with the aglycone. Thermodynamic studies established that normal phase and reversed phase enantioseparations were enthalpy-driven. With polar waterless mobile phases used in the polar ionic mode, some separations were enthalpy-driven and others were entropy-driven. The linear solvation energy method was tentatively used to gain knowledge about the chiral recognition mechanism. It appeared to be a viable approach with neutral molecules but it failed with ionizable solutes. With molecular solutes and the teicoplanin CSP, the study showed a significant role of the surface charge-induced dipole interaction and steric effects. The remarkable complementary enantioselectivity effect observed with the four CSPs is discussed.     

Sepsis: molecular mechanisms underlying lipopolysaccharide recognition

Sepsis is an often-fatal response of the immune system against microbial pathogens. The molecular mechanisms that have been designed to protect the host from invading pathogens are responsible for the damage and injury. It is now widely known that this crucial response of the immune system is mediated by innate immunity, which employs a plethora of pattern recognition receptors that recognise motifs expressed by pathogens. A lack of knowledge of the mediators involved in innate recognition has led to unsuccessful attempts at designing effective therapeutic interventions for sepsis. However, in recent years, great leaps forward have been achieved in our knowledge of these mediators. In this review we attempt to unravel the molecular mechanisms underlying bacterial recognition, particularly recognition of bacterial lipopolysaccharide, and we propose future potential therapeutic targets for septic shock.     

Action anticipation in human infants reveals assumptions about anteroposterior body-structure and action

Animal actions are almost universally constrained by the bilateral body-plan. For example, the direction of travel tends to be constrained by the orientation of the animal''s anteroposterior axis. Hence, an animal''s behaviour can reliably guide the identification of its front and back, and its orientation can reliably guide action prediction. We examine the hypothesis that the evolutionarily ancient relation between anteroposterior body-structure and behaviour guides our cognitive processing of agents and their actions. In a series of studies, we demonstrate that, after limited exposure, human infants as young as six months of age spontaneously encode a novel agent as having a certain axial direction with respect to its actions and rely on it when anticipating the agent''s further behaviour. We found that such encoding is restricted to objects exhibiting cues of agency and does not depend on generalization from features of familiar animals. Our research offers a new tool for investigating the perception of animate agency and supports the proposal that the underlying cognitive mechanisms have been shaped by basic biological adaptations in humans.