What does 'chromatin remodeling' mean?

The regulated alteration of chromatin structure, termed 'chromatin remodeling', can be accomplished by covalent modification of histones or by the action of ATP-dependent remodeling complexes. A variety of mechanisms can be used to remodel chromatin; some act locally on a single nucleosome and others act more broadly. It is critical to establish a direct connection between the remodeling events observed in vivo and the mechanistic capabilities of remodeling complexes in vitro.     

What do we mean by biological complexity?

The purpose of the present paper is to offer a precise definition of the concepts of integration, emergence and complexity in biological networks through the use of the information theory. If two distinct properties of a network are expressed by two discrete variables, the classical subadditivity principle of Shannon's information theory applies when all the nodes of the network are associated with these properties. If not, the subadditivity principle may not apply. This situation is often to be encountered with enzyme and metabolic networks, for some nodes may well not be associated with these two properties. This is precisely what is occurring with an enzyme that binds randomly its two substrates. This situation implies that an enzyme, or a metabolic network, may display a joint entropy equal, smaller, or larger than the corresponding sum of individual entropies of component sub-systems. In the first case, the collective properties of the network can be reduced to the individual properties of its components. Moreover, the network is devoid of any information. In the second case, the system displays integration effects, behaves as a coherent whole, and has positive information. But if the joint entropy of the network is smaller than the sum of the individual entropies of its components, then the system has emergent collective properties and can be considered complex. Moreover, under these conditions, its information is negative. The extent of negative information is enhanced if the enzyme, or the metabolic network, is far away from equilibrium.     

What does "plasmid biology" currently mean? Summary of the Plasmid Biology 2004 Meeting

Almost 200 scientists from America, Europe, Asia, Australia, and Africa participated in the Plasmid Biology 2004 meeting, which was organized between 15th and 21st September 2004 in Kanoni (Corfu island), Greece. Various aspects of biology of plasmids and other mobile genetic elements were discussed during the meeting, including problems of replication, transfer, stable inheritance, and evolution. Medical and veterinary aspects of plasmids were highlighted as well as other applications of these replicons. It appears that plasmids and other mobile genetic elements are still excellent models in studies of basic biological problems at the molecular level, and their role in medicine and genetic engineering can be enormous. Moreover, studies on ecology of plasmids provide extremely important data that can be used in environment protection as well as in biotechnology. Understanding the importance of studies on plasmids and other mobile genetic elements, participants of the meeting decided to establish the International Society for Plasmid Biology.     

What does 'biodiversity' mean - scientific problem or convenient myth?

Biodiversity has become an everyday word, not just for ecologists but for politicians, the media and the general public too. But does It have a genuine scientific meaning that distinguishes it from earlier studies of diversity, or has it assumed a mythological status?     

What does it mean to identify a protein in proteomics?

The annotation of the human genome indicates the surprisingly low number of approximately 40,000 genes. However, the estimated number of proteins encoded by these genes is two to three orders of magnitude higher. The ability to unambiguously identify the proteins is a prerequisite for their functional investigation. As proteins derived from the same gene can be largely identical, and might differ only in small but functionally relevant details, protein identification tools must not only identify a large number of proteins but also be able to differentiate between close relatives. This information can be generated by mass spectrometry, an approach that identifies proteins by partial analysis of their digestion-derived peptides. Information gleaned from databases fills in the missing sequence information. Because both sequence databases and experimental data are limited, a certain ambiguity often remains concerning which sequence variant(s) and modification(s) are present. As the common denominator of all the isoforms is a gene, in our opinion, it would be more accurate to state that a product of this particular gene rather than a certain protein has been identified by mass spectrometry.     

Response to commentary: does before bedtime body warming by bathing or other means attenuate sleep-time arterial blood pressure?

ABSTRACT

The commentary by Dr. Smolensky provides an insightful assessment of our study from the circadian point of view. In the present letter, we have responded to the commentary by Dr. Smolensky et al., suggesting interpretation of our analytic results and providing additional statistical data regarding the timing of antihypertensive drug use. In addition, we have discussed the terms “nighttime” and “sleep-time” period used in previous researches in relation to ambulatory blood pressure.     

Modulating social behavior with oxytocin: How does it work? What does it mean?

Among its many roles in body and brain, oxytocin influences social behavior. Understanding the precise nature of this influence is crucial, both within the broader theoretical context of neurobiology, social neuroscience and brain evolution, but also within a clinical context of disorders such as anxiety, schizophrenia, and autism. Research exploring oxytocin's role in human social behavior is difficult owing to its release in both body and brain and its interactive effects with other hormones and neuromodulators. Additional difficulties are due to the intricacies of the blood-brain barrier and oxytocin's instability, which creates measurement issues. Questions concerning how to interpret behavioral results of human experiments manipulating oxytocin are thus made all the more pressing. The current paper discusses several such questions. We highlight unresolved fundamental issues about what exactly happens when oxytocin is administered intranasally, whether such oxytocin does in fact reach appropriate receptors in brain, and whether central or peripheral influences account for the observed behavioral effects. We also highlight the deeper conceptual issue of whether the human data should be narrowly interpreted as implicating a specific role for oxytocin in complex social cognition, such a generosity, trust, or mentalizing, or more broadly interpreted as implicating a lower-level general effect on general states and dispositions, such as anxiety and social motivation. Using several influential studies, we show how seemingly specific, higher-level social-cognitive effects can emerge via a process by which oxytocin's broad influence is channeled into a specific social behavior in a context of an appropriate social and research setting. This article is part of a Special Issue entitled Oxytocin, Vasopressin, and Social Behavior.     

What does "arboreal locomotion" mean exactly and what are the relationships between "climbing", environment and morphology?

The characteristics of "climbing" in the sense of locomotion or posture on three-dimensional substrates are discussed from a biomechanical viewpoint. For this purpose, the mechanical conditions of the most widely spread modes of locomotion or gaits used in arboreal surroundings are reviewed. This allows precise identification of morphological characteristics of traits that are advantageous, and therefore have a positive selective value. Further, at least some of the environmental and substrate characteristics that need to be present for using a specific gait, are noted. It turns out that the extremity which is placed lower on the substrate, has to carry a higher load. If this extremity is consistently the hindlimb--which actually is the case in primates, because of understandable, though complex reasons--a division of labor is likely to occur between the limbs: the hindlimb becoming stronger and the forelimb weaker, but more versatile. A very specific, and advantageous feature of the primates is their possession of prehensile hands and feet. That means the autopodia are able (1) to produce by themselves, without the aid of body weight, very high frictional resistance, and (2) to transmit tensile forces as well as torsional moments on the substrate. The above-mentioned division of labor between fore- and hindlimbs implies that the former make the first contacts with and explore the properties of parts of the environment. As a next step, prehensile hands on long arms may easily replace length and mobility of the neck in getting hold of food items. So very characteristic traits of human body shape can be derived to a large extent from the necessities of arboreal locomotion: Prehensile hands, long arms, concentration of body weight on the hindlimbs, shortness of the trunk in comparison to limb length.     

The equilibrium concept and density dependence tests What does it all mean?

Summary Tests of density dependent regulation of population size depend on the concept of equilibrium population size. Such an equilibrium is a purely theoretical construct whose existence in the field is debatable and whose value cannot be measured. An equilibrium is supposed to fluctuate in time, but the extent of the fluctuations relative to those of the population size is unknowable. It is impossible to separate a fluctuating population size from a fluctuating equilibrium value and from fluctuating deviations from an equilibrium value. Because it cannot be determined whether a given population size is above, at, or below equilibrium, the course of population size in unpredictable and density dependence tests cannot be expected to produce useful results. Stabilization tests may provide a more useful alternative.