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 does the homology between E. coli tRNAs and RNAs controlling ColE1 plasmid replication mean?

Nucleotide sequences of E. coli tRNAs and RNA I or RNA II (controlling replication of ColE1 plasmids) were compared using the computer. The homology between some of these molecules is over 60%. The distribution of homologous nucleotides among the functional elements (stems and loops) of either RNA I or RNA II and the tRNAs molecules was studied. It was found that the homologous domains are located mainly in the loop regions of RNA I or RNA II. A consensus sequence, the nonanucleotide AGUUGGUAG, was discovered in loop II of RNA I and in the dihydrouridylic loop of tRNAs showing homology with RNA I. Based on this observation, a hypothesis was drawn for a possible role of the tRNAs in the regulation of plasmid DNA replication.     

What does geometric mean,mean geometrically? Assessing the utility of geometric mean and other size variables in studies of skull allometry

This study investigated the effects of using different size variables for interpretations of relative orbit size and mandibular robusticity. Thirty-three skull measurements taken on 385 platyrrhines representing 12 of 16 New World monkey genera (in addition to body mass and total body length) were used singly and in combinations (by taking the geometric mean of all measurements) as size variables to produce relative size indices of orbit area and mandibular thickness. These indices were then compared to investigate which size variables proved effective at differentiating nocturnal from diurnal taxa and hard object from soft object feeders based upon results from previous biomechanical studies. It was found that certain groups of size variables consistently produced the a priori expectations and resulted in lower coefficients of variation. The general principles shared by these size variables were that they sampled anatomically remote regions of the skull that appear to be functionally independent from the trait being evaluated and they were nearly always geometric mean combinations composed of a relatively high number (>or=12) of large measurements. Suggestions are also presented for amending these principles for use with incomplete material such as fossils.     

What does the "screening hypochromism of chromophores" actually imply?

Comments to the article of N.L. Vekshin "Screening hypochromism of chromophores in macromolecular biostructures (Biophysics, 1999. V. 44. P. 45.) are given. The incorrectness of the main propositions and results of the study is shown.     

What does one mean by "arterial blood oxygenation?"

We used the following question in a large classroom session attended by undergraduate medical students and doctors with a Bachelor of Medicine and Bachelor of Surgery (MBBS) degree (240 in all) to test for conceptual understanding as to what constitutes arterial blood oxygenation. The question read as follows: Which one of the following physiological parameters taken alone tells you that arterial blood oxygenation in a critically ill patient is satisfactory? A. (Alveolar-arterial) O(2) gradient=10 mmHg. B. Partial pressure of O(2) in arterial blood=95 mmHg. C. O(2)saturation of hemoglobin>90%. D. Blood hemoglobin concentration=12 g/dl. Only 25 of 240 students correctly indicated that none of the above parameters taken alone could give us this information. Once students turned in their answers, we presented five examples illustrating how none of the above answers could be used alone to assess arterial blood oxygenation. Students were then asked to provide written feedback on their understanding of this topic. The majority of students indicated that they were satisfied that they got rid of a misconception.     

What does a common channel for electrolytes and non-electrolytes in the sperm mean?

Cell volume is central to osmoregulation in intact cells. Bovine spermatozoa, as also other mammalian spermatozoa, exhibit a very rapid regulatory volume decrease (RVD) when exposed to hypotonic saline media. This response, fastest known in animal cells, is mediated by a putative potassium channel which the pharmacological properties of a conventional channel and yet admits both electrolytes and non-electrolytes. The evolutionary basis and functional role of this conserved quinine-sensitive channel in mammalian sperm could offer hitherto unexplored facets of the link(s) between ecology and reproduction.     

Will the "new biology" affect the future of histopathology?

The technologies used in histopathology are changing as a consequence of the current revolutionary progress in several areas of biology. It is likely that general cancer management will improve because of the impact of molecular techniques and immunohistochemistry on tumor diagnosis and classification and on the determination of prognosis and response to therapy. Moreover, as therapies are starting to be modelled after the distinctive molecular characteristics of a specific tumor, the availability of molecular tests to all patients will become a matter of great importance.     

Who does all the research in conservation biology?

Much of the worlds biodiversity is located within countries with developing economies. We therefore examine how well developing nations and their scientists are represented in three international conservation biology journals (Conservation Biology, Biological Conservation, Biodiversity and Conservation). We found: (1) that 28% of studies were from lower income countries and only 15% of all papers had primary authors from these nations. Of papers from lower income countries, although 80% had at least one local author, only 47% had primary authors from the country where the study was conducted. (2) Lower income countries had more research with a strong applied focus compared to research from high-income countries. (3) In lower income countries research was often funded by international sources but the primary authors of these studies were from affluent nations. (4) The three journals differed in how well they represented lower income nations and their scientists, reflecting their editorial policies for including research from lower income nations. The main reason for the large discrepancy in a countrys output of conservation research is due to the difference in a nations ability to invest in science. However, a brief survey of authors suggests that there is a large amount of information available in lower income and non-English speaking countries that is not easily accessible to the international conservation community. Journals may therefore need to consider altering their policies if we are to improve the representation of research by scientists in lower income nations.     

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 philosophy of modelling or does the philosophy of biology have any use?

Biologists in search of answers to real-world issues such as the ecological consequences of global warming, the design of species'' conservation plans, understanding landscape dynamics and understanding gene expression make decisions constantly that are based on a ‘philosophical’ stance as to how to create and test explanations of an observed phenomenon. For better or for worse, some kind of philosophy is an integral part of the doing of biology. Given this, it is more important than ever to undertake a practical assessment of what philosophy does mean and should mean to biologists. Here, I address three questions: should biologists pay any attention to ‘philosophy’; should biologists pay any attention to ‘philosophy of biology’; and should biologists pay any attention to the philosophy of biology literature on modelling? I describe why the last question is easily answered affirmatively, with the proviso that the practical benefits to be gained by biologists from this literature will be directly proportional to the extent to which biologists understand ‘philosophy’ to be a part of biology, not apart from 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.     

What lies at the interface of regenerative medicine and developmental biology?

At a recent Keystone Symposium on 'Developmental Biology and Tissue Engineering', new findings in areas ranging from stem cell differentiation, embryonic pattern formation and organ regeneration to engineered cell microenvironments, synthetic biomaterials and artificial tissue fabrication were described. Although these new advances were exciting, this symposium clarified that biologists and engineers often view the challenge of tissue formation from different, and sometimes conflicting, perspectives. These dichotomies raise questions regarding the definition of regenerative medicine, but offer the promise of exciting new interdisciplinary approaches to tissue and organ regeneration, if effective alliances can be established.